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 9PDK | pdb_00009pdk

Composite map of closed form of PIC-Med-SWI/SNF

External Resource: Annotation


Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
DB [auth sF],
I [auth B8],
ND [auth SF],
SB [auth A8]		PF04855SNF5 / SMARCB1 / INI1 (SNF5)SNF5 / SMARCB1 / INI1- Family
H [auth B7],
RB [auth A7]		PF13625Helicase conserved C-terminal domain (Helicase_C_3)Helicase conserved C-terminal domainThis domain family is found in a wide variety of helicases and helicase-related proteins. Domain
H [auth B7],
RB [auth A7]		PF04851Type III restriction enzyme, res subunit (ResIII)Type III restriction enzyme, res subunit- Family
H [auth B7],
RB [auth A7]		PF16203ERCC3/RAD25/XPB C-terminal helicase (ERCC3_RAD25_C)ERCC3/RAD25/XPB C-terminal helicaseThis is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases [1]. Domain
G [auth B6],
QB [auth A6]		PF04056Ssl1-like (Ssl1)Ssl1-likeSsl1-like proteins are 40kDa subunits of the Transcription factor II H complex. Domain
G [auth B6],
QB [auth A6]		PF07975TFIIH C1-like domain (C1_4)TFIIH C1-like domainThe carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD ...The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (Pfam:PF00130) [1].
Domain
FE [auth t6],
ZD [auth T6]		PF20719Mediator complex subunit 16, C-terminal (Med16_C)Mediator complex subunit 16, C-terminalMed16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression [2]. This is the small alpha-beta domain found at the C-terminal of Mediator complex subunit 16 [1]. Domain
FE [auth t6],
ZD [auth T6]		PF11635Mediator complex subunit 16, N-terminal (Med16_N)Mediator complex subunit 16, N-terminal- Repeat
BE [auth t2],
VD [auth T2]		PF11593Mediator complex subunit 3 fungal (Med3)Mediator complex subunit 3 fungal- Family
JB [auth sL],
TD [auth SL]		PF00022Actin (Actin)Actin- Family
IB [auth sK],
SD [auth SK]		PF00022Actin (Actin)Actin- Family
HB [auth sJ],
RD [auth SJ]		PF09510Rtt102p-like transcription regulator protein (Rtt102p)Rtt102p-like transcription regulator protein- Family
CB [auth sE],
MD [auth SE]		PF08624Chromatin remodelling complex Rsc7/Swp82 subunit (CRC_subunit)Chromatin remodelling complex Rsc7/Swp82 subunit- Family
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		PF00249Myb-like DNA-binding domain (Myb_DNA-binding)Myb-like DNA-binding domainThis family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1]. Domain
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		PF16495SWIRM-associated region 1 (SWIRM-assoc_1)SWIRM-associated region 1- Family
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		PF04433SWIRM domain (SWIRM)SWIRM domainThis SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA [1]. Domain
E [auth B4],
OB [auth A4]		PF03850Transcription factor Tfb4 (Tfb4)Transcription factor Tfb4This family appears to be distantly related to the VWA domain. Domain
D [auth B3],
NB [auth A3]		PF17121Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_5)Zinc finger, C3HC4 type (RING finger)Domain
D [auth B3],
NB [auth A3]		PF06391CDK-activating kinase assembly factor MAT1 (MAT1)CDK-activating kinase assembly factor MAT1- Family
GA [auth BX],
QC [auth AX]		PF18121TFA2 Winged helix domain 2 (TFA2_Winged_2)TFA2 Winged helix domain 2This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase [1]. Domain
GA [auth BX],
QC [auth AX]		PF02186TFIIE beta subunit core domain (TFIIE_beta)TFIIE beta subunit core domainGeneral transcription factor TFIIE consists of two subunits, TFIIE alpha Pfam:PF02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymer ...General transcription factor TFIIE consists of two subunits, TFIIE alpha Pfam:PF02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved [1] and has a winged helix fold.
Domain
GA [auth BX],
QC [auth AX]		PF22254Tfa2 E-tether (TFA2_E-tether)Tfa2 E-tetherThe small TFIIE subunit Tfa2 (yeast TFIIE-beta) contains two WH domains and two conserved alpha-helices called the E-tether [1] that bind the E-linker. Consistent with the structure, the E-tether is essential for TFIIE function and subunit dimerisati ...The small TFIIE subunit Tfa2 (yeast TFIIE-beta) contains two WH domains and two conserved alpha-helices called the E-tether [1] that bind the E-linker. Consistent with the structure, the E-tether is essential for TFIIE function and subunit dimerisation. Members of this group are found in fungi.
Domain
FA [auth BW],
PC [auth AW]		PF02002TFIIE alpha subunit (TFIIE_alpha)TFIIE alpha subunitThe general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha Swiss:P29083 and TFIIE-beta Swiss:P29084 a ...The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha Swiss:P29083 and TFIIE-beta Swiss:P29084 and joins the pre-initiation complex after RNA polymerase II and TFIIF [1]. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha [2] and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also Swiss:O29501 [3].
Domain
EA [auth BV],
OC [auth AV]		PF02751Transcription initiation factor IIA, gamma subunit (TFIIA_gamma_C)Transcription initiation factor IIA, gamma subunitAccurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA bo ...Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel.
Domain
EA [auth BV],
OC [auth AV]		PF02268Transcription initiation factor IIA, gamma subunit, helical domain (TFIIA_gamma_N)Transcription initiation factor IIA, gamma subunit, helical domainAccurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA ...Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle.
Domain
DA [auth BU],
NC [auth AU]		PF03153Transcription factor IIA, alpha/beta subunit (TFIIA)Transcription factor IIA, alpha/beta subunit- Family
C [auth B2],
MB [auth A2]		PF03849Transcription factor Tfb2 (Tfb2)Transcription factor Tfb2- Family
C [auth B2],
MB [auth A2]		PF18307Transcription factor Tfb2 (p52) C-terminal domain (Tfb2_C)Transcription factor Tfb2 (p52) C-terminal domainThis is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH arc ...This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH architecture and TFIIHs function in nucleotide-excision repair (NER) pathway. The C-terminal domain of Tfb2 is thought to have a crucial role in DNA repair [1].
Domain
BA [auth BS],
LC [auth AS]		PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)Domain
AA [auth BR],
KC [auth AR]		PF02270TFIIF, beta subunit HTH domain (TFIIF_beta)TFIIF, beta subunit HTH domainAccurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which in ...Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter.
Domain
AA [auth BR],
KC [auth AR]		PF17683TFIIF, beta subunit N-terminus (TFIIF_beta_N)TFIIF, beta subunit N-terminus- Family
IC [auth AO],
Y [auth BO]		PF00352Transcription factor TFIID (or TATA-binding protein, TBP) (TBP)Transcription factor TFIID (or TATA-binding protein, TBP)Domain
GC [auth AM],
W [auth BM]		PF00382Transcription factor TFIIB repeat (TFIIB)Transcription factor TFIIB repeatDomain
GC [auth AM],
W [auth BM]		PF08271TFIIB zinc-binding (Zn_Ribbon_TF)TFIIB zinc-bindingThe transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ...The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure [1].
Domain
FC [auth AL],
V [auth BL]		PF03604DNA directed RNA polymerase, 7 kDa subunit (Zn_ribbon_RPAB4)DNA directed RNA polymerase, 7 kDa subunitDomain
EC [auth AK],
U [auth BK]		PF13656RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)RNA polymerase Rpb3/Rpb11 dimerisation domainThe two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.
Domain
DC [auth AJ],
T [auth BJ]		PF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunitDomain
B [auth B1],
LB [auth A1]		PF03909BSD domain (BSD)BSD domainThis domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function. Domain
CC [auth AI],
S [auth BI]		PF02150RNA polymerases M/15 Kd subunit (Zn_ribbon_RPB9)RNA polymerases M/15 Kd subunitDomain
CC [auth AI],
S [auth BI]		PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)Domain
BC [auth AH],
R [auth BH]		PF03870RNA polymerase Rpb8 (RNA_pol_Rpb8)RNA polymerase Rpb8- Family
AC [auth AG],
Q [auth BG]		PF03876SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].
Domain
AC [auth AG],
Q [auth BG]		PF00575S1 RNA binding domain (S1)S1 RNA binding domainThe S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Domain
P [auth BF],
ZB [auth AF]		PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
O [auth BE],
YB [auth AE]		PF01191RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)RNA polymerase Rpb5, C-terminal domainThe assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. Domain
O [auth BE],
YB [auth AE]		PF03871RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)RNA polymerase Rpb5, N-terminal domainRpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ...Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA.
Domain
N [auth BD],
XB [auth AD]		PF03874RNA polymerase Rpb4 (RNA_pol_Rpb4)RNA polymerase Rpb4- Family
M [auth BC],
WB [auth AC]		PF01193RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)RNA polymerase Rpb3/Rpb11 dimerisation domainThe two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.
Domain
M [auth BC],
WB [auth AC]		PF01000RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)RNA polymerase Rpb3/RpoA insert domainMembers of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal Domain
L [auth BB],
VB [auth AB]		PF04561RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)RNA polymerase Rpb2, domain 2RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Domain
L [auth BB],
VB [auth AB]		PF04560RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)RNA polymerase Rpb2, domain 7RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].
Domain
L [auth BB],
VB [auth AB]		PF04565RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)RNA polymerase Rpb2, domain 3RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].
Domain
L [auth BB],
VB [auth AB]		PF04566RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)RNA polymerase Rpb2, domain 4RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1].
Domain
L [auth BB],
VB [auth AB]		PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
L [auth BB],
VB [auth AB]		PF00562RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)RNA polymerase Rpb2, domain 6RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Domain
L [auth BB],
VB [auth AB]		PF04567RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)RNA polymerase Rpb2, domain 5RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].
Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		PF00623RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)RNA polymerase Rpb1, domain 2RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].
Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		PF05001RNA polymerase Rpb1 C-terminal repeat (RNA_pol_Rpb1_R)RNA polymerase Rpb1 C-terminal repeat- Repeat
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		PF04990RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)RNA polymerase Rpb1, domain 7RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile modu ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2].
Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		PF05000RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)RNA polymerase Rpb1, domain 4RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].
Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		PF04983RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)RNA polymerase Rpb1, domain 3RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].
Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		PF04992RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)RNA polymerase Rpb1, domain 6RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile modu ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II.
Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		PF04998RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)RNA polymerase Rpb1, domain 5RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].
Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		PF04997RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)RNA polymerase Rpb1, domain 1RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp dom ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].
Domain
J [auth B9],
TB [auth A9]		PF17035Bromodomain extra-terminal - transcription regulation (BET)Bromodomain extra-terminal - transcription regulationThe BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impa ...The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins [1].
Domain
A [auth B0],
KB [auth A0]		PF13307Helicase C-terminal domain (Helicase_C_2)Helicase C-terminal domainThis domain is found at the C-terminus of DEAD-box helicases. Domain
A [auth B0],
KB [auth A0]		PF06777Helical and beta-bridge domain (HBB)Helical and beta-bridge domainHBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein ...HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein verifies the presence of damage to DNA and allows DNA repair to proceed. XPD is an assembly of several domains to form a doughnut-shaped molecule that is able to separate two DNA strands and scan the DNA for damage. HBB helps to form the overall DNA-clamping architecture [1]. This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-).
Domain
A [auth B0],
KB [auth A0]		PF06733DEAD_2 (DEAD_2)DEAD_2- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DB [auth sF],
I [auth B8],
ND [auth SF],
SB [auth A8]		SWI/SNF chromatin-remodeling complex subunit SNF5
H [auth B7],
RB [auth A7]		General transcription and DNA repair factor IIH helicase subunit XPB
G [auth B6],
QB [auth A6]		General transcription and DNA repair factor IIH subunit SSL1
FE [auth t6],
ZD [auth T6]		Mediator of RNA polymerase II transcription subunit 16
EE [auth t5],
YD [auth T5]		Mediator of RNA polymerase II transcription subunit 15
CE [auth t3],
WD [auth T3]		Mediator of RNA polymerase II transcription subunit 5
BE [auth t2],
VD [auth T2]		Mediator of RNA polymerase II transcription subunit 3
AE [auth t1],
UD [auth T1]		Mediator of RNA polymerase II transcription subunit 2
F [auth B5],
PB [auth A5]		General transcription and DNA repair factor IIH subunit TFB5-
JB [auth sL],
TD [auth SL]		Actin-like protein ARP9
IB [auth sK],
SD [auth SK]		Actin-related protein 7
HB [auth sJ],
RD [auth SJ]		Regulator of Ty1 transposition protein 102
GB [auth sI],
QD [auth SI]		SWI/SNF chromatin-remodeling complex subunit SWI1
FB [auth sH],
PD [auth SH]		Transcription regulatory protein SNF2
EB [auth sG],
OD [auth SG]		unsigned peptide of SWISNF---
CB [auth sE],
MD [auth SE]		SWI/SNF global transcription activator complex subunit SWP82
AB [auth sC],
KD [auth SC]		Transcription regulatory protein SNF6
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		SWI/SNF complex subunit SWI3
ID [auth SA],
YA [auth sA]		Transcription regulatory protein SNF12
E [auth B4],
OB [auth A4]		General transcription and DNA repair factor IIH subunit TFB4
HD [auth Mp],
XA [auth mp]		Mediator of RNA polymerase II transcription subunit 1
GD [auth Mo],
WA [auth mo]		Mediator of RNA polymerase II transcription subunit 31
FD [auth Mn],
VA [auth mn]		Mediator of RNA polymerase II transcription subunit 21
ED [auth Mm],
UA [auth mm]		Mediator of RNA polymerase II transcription subunit 19
DD [auth Ml],
DE [auth t4],
TA [auth ml],
XD [auth T4]		Mediator of RNA polymerase II transcription subunit 14
CD [auth Mk],
SA [auth mk]		Mediator of RNA polymerase II transcription subunit 10
BD [auth Mj],
RA [auth mj]		Mediator of RNA polymerase II transcription subunit 9
AD [auth Mi],
QA [auth mi]		Mediator of RNA polymerase II transcription subunit 7
PA [auth mh],
ZC [auth Mh]		Mediator of RNA polymerase II transcription subunit 4
OA [auth mg],
YC [auth Mg]		Mediator of RNA polymerase II transcription subunit 22
D [auth B3],
NB [auth A3]		RNA polymerase II transcription factor B subunit 3
NA [auth mf],
XC [auth Mf]		Mediator of RNA polymerase II transcription subunit 20
MA [auth me],
WC [auth Me]		Mediator of RNA polymerase II transcription subunit 18
LA [auth md],
VC [auth Md]		Mediator of RNA polymerase II transcription subunit 17
KA [auth mc],
UC [auth Mc]		Mediator of RNA polymerase II transcription subunit 11
JA [auth mb],
TC [auth Mb]		Mediator of RNA polymerase II transcription subunit 8
IA [auth ma],
SC [auth Ma]		Mediator of RNA polymerase II transcription subunit 6
GA [auth BX],
QC [auth AX]		Transcription initiation factor IIE subunit beta
FA [auth BW],
PC [auth AW]		Transcription initiation factor IIE subunit alpha
EA [auth BV],
OC [auth AV]		Transcription initiation factor IIA subunit 2
DA [auth BU],
NC [auth AU]		Transcription initiation factor IIA large subunit
C [auth B2],
MB [auth A2]		General transcription and DNA repair factor IIH subunit TFB2
CA [auth BT],
MC [auth AT]		promoter DNA---
BA [auth BS],
LC [auth AS]		Transcription elongation factor S-II
AA [auth BR],
KC [auth AR]		Transcription initiation factor IIF subunit beta
JC [auth AQ],
Z [auth BQ]		Transcription initiation factor IIF subunit alpha
IC [auth AO],
Y [auth BO]		TATA-box-binding protein
HC [auth AN],
X [auth BN]		promoter DNA---
GC [auth AM],
W [auth BM]		Transcription initiation factor IIB
FC [auth AL],
V [auth BL]		DNA-directed RNA polymerases I, II, and III subunit RPABC4
EC [auth AK],
U [auth BK]		DNA-directed RNA polymerase II subunit RPB11
DC [auth AJ],
T [auth BJ]		DNA-directed RNA polymerases I, II, and III subunit RPABC5
B [auth B1],
LB [auth A1]		General transcription and DNA repair factor IIH subunit TFB1
CC [auth AI],
S [auth BI]		DNA-directed RNA polymerase II subunit RPB9
BC [auth AH],
R [auth BH]		DNA-directed RNA polymerases I, II, and III subunit RPABC3
AC [auth AG],
Q [auth BG]		DNA-directed RNA polymerase II subunit RPB7
P [auth BF],
ZB [auth AF]		DNA-directed RNA polymerases I, II, and III subunit RPABC2
O [auth BE],
YB [auth AE]		DNA-directed RNA polymerases I, II, and III subunit RPABC1
N [auth BD],
XB [auth AD]		DNA-directed RNA polymerase II subunit RPB4
M [auth BC],
WB [auth AC]		DNA-directed RNA polymerase II subunit RPB3
L [auth BB],
VB [auth AB]		DNA-directed RNA polymerase II subunit RPB2
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		DNA-directed RNA polymerase II subunit RPB1
J [auth B9],
TB [auth A9]		Transcription initiation factor TFIID subunit 14
A [auth B0],
KB [auth A0]		General transcription and DNA repair factor IIH helicase subunit XPD/RAD3

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
DB [auth sF],
I [auth B8],
ND [auth SF],
SB [auth A8]		IPR006939SNF5/SMARCB1/INI1Family
H [auth B7],
RB [auth A7]		IPR032830Helicase XPB/Ssl2, N-terminal domainDomain
H [auth B7],
RB [auth A7]		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
H [auth B7],
RB [auth A7]		IPR006935Helicase/UvrB, N-terminalDomain
H [auth B7],
RB [auth A7]		IPR001650Helicase, C-terminal domain-likeDomain
H [auth B7],
RB [auth A7]		IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
H [auth B7],
RB [auth A7]		IPR032438ERCC3/RAD25/XPB helicase, C-terminal domainDomain
H [auth B7],
RB [auth A7]		IPR001161Helicase XPB/Ssl2Family
H [auth B7],
RB [auth A7]		IPR050615ATP-dependent DNA HelicaseFamily
G [auth B6],
QB [auth A6]		IPR007198Ssl1-likeDomain
G [auth B6],
QB [auth A6]		IPR012170TFIIH subunit Ssl1/p44Family
G [auth B6],
QB [auth A6]		IPR004595TFIIH C1-like domainDomain
G [auth B6],
QB [auth A6]		IPR013087Zinc finger C2H2-typeDomain
G [auth B6],
QB [auth A6]		IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
G [auth B6],
QB [auth A6]		IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
G [auth B6],
QB [auth A6]		IPR002035von Willebrand factor, type ADomain
G [auth B6],
QB [auth A6]		IPR046349C1-like domain superfamilyHomologous Superfamily
FE [auth t6],
ZD [auth T6]		IPR048338Mediator complex, subunit Med16Family
FE [auth t6],
ZD [auth T6]		IPR048339Mediator complex subunit 16, C-terminalDomain
FE [auth t6],
ZD [auth T6]		IPR021665Mediator complex, subunit Med16, N-terminalDomain
EE [auth t5],
YD [auth T5]		IPR008626Mediator complex, subunit Med15, fungiFamily
EE [auth t5],
YD [auth T5]		IPR033789Gal11, coactivator domainDomain
EE [auth t5],
YD [auth T5]		IPR036529Coactivator CBP, KIX domain superfamilyHomologous Superfamily
EE [auth t5],
YD [auth T5]		IPR036546Mediator complex subunit 15, KIX domainDomain
CE [auth t3],
WD [auth T3]		IPR014801Mediator complex, subunit Med5, fungiFamily
BE [auth t2],
VD [auth T2]		IPR020998Mediator of RNA polymerase II transcription subunit 3Family
AE [auth t1],
UD [auth T1]		IPR021017Mediator complex, subunit Med2, fungiFamily
F [auth B5],
PB [auth A5]		IPR009400TFIIH subunit TTDA/Tfb5Family
F [auth B5],
PB [auth A5]		IPR035935TFB5-like superfamilyHomologous Superfamily
JB [auth sL],
TD [auth SL]		IPR043129ATPase, nucleotide binding domainHomologous Superfamily
JB [auth sL],
TD [auth SL]		IPR004000Actin familyFamily
IB [auth sK],
SD [auth SK]		IPR043129ATPase, nucleotide binding domainHomologous Superfamily
IB [auth sK],
SD [auth SK]		IPR004000Actin familyFamily
HB [auth sJ],
RD [auth SJ]		IPR018304Transcription regulator protein Rtt102Family
GB [auth sI],
QD [auth SI]		IPR051232ARID/SWI1_ChromRemodUnknown
GB [auth sI],
QD [auth SI]		IPR001606ARID DNA-binding domainDomain
GB [auth sI],
QD [auth SI]		IPR036431ARID DNA-binding domain superfamilyHomologous Superfamily
FB [auth sH],
PD [auth SH]		IPR018359Bromodomain, conserved siteConserved Site
FB [auth sH],
PD [auth SH]		IPR001487BromodomainDomain
FB [auth sH],
PD [auth SH]		IPR049730SNF2/RAD5-like, C-terminal helicase domainDomain
FB [auth sH],
PD [auth SH]		IPR014978Glutamine-Leucine-Glutamine, QLQDomain
FB [auth sH],
PD [auth SH]		IPR038718SNF2-like, N-terminal domain superfamilyHomologous Superfamily
FB [auth sH],
PD [auth SH]		IPR000330SNF2, N-terminal domainDomain
FB [auth sH],
PD [auth SH]		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
FB [auth sH],
PD [auth SH]		IPR001650Helicase, C-terminal domain-likeDomain
FB [auth sH],
PD [auth SH]		IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
FB [auth sH],
PD [auth SH]		IPR036427Bromodomain-like superfamilyHomologous Superfamily
FB [auth sH],
PD [auth SH]		IPR017956AT hook, DNA-binding motifConserved Site
FB [auth sH],
PD [auth SH]		IPR014012Helicase/SANT-associated domainDomain
FB [auth sH],
PD [auth SH]		IPR029295Snf2, ATP coupling domainDomain
CB [auth sE],
MD [auth SE]		IPR013933Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82Family
AB [auth sC],
KD [auth SC]		IPR059172Transcription regulatory protein SNF6Domain
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		IPR009057Homeodomain-like superfamilyHomologous Superfamily
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		IPR017884SANT domainDomain
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		IPR001005SANT/Myb domainDomain
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		IPR007526SWIRM domainDomain
BB [auth sD],
JD [auth SB],
LD [auth SD],
ZA [auth sB]		IPR032451SMARCC, C-terminalDomain
ID [auth SA],
YA [auth sA]		IPR036885SWIB/MDM2 domain superfamilyHomologous Superfamily
ID [auth SA],
YA [auth sA]		IPR063302SWIFT domainDomain
E [auth B4],
OB [auth A4]		IPR004600TFIIH subunit Tfb4/GTF2H3Family
E [auth B4],
OB [auth A4]		IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
HD [auth Mp],
XA [auth mp]		IPR019680Mediator complex, subunit Med1Domain
GD [auth Mo],
WA [auth mo]		IPR008831Mediator complex, subunit Med31Family
GD [auth Mo],
WA [auth mo]		IPR038089Mediator of RNA polymerase II, subunit Med31 superfamilyHomologous Superfamily
FD [auth Mn],
VA [auth mn]		IPR037212Mediator complex, subunit Med7/Med21-likeHomologous Superfamily
FD [auth Mn],
VA [auth mn]		IPR021384Mediator complex, subunit Med21Family
ED [auth Mm],
UA [auth mm]		IPR013942Mediator complex, subunit Med19, fungiFamily
DD [auth Ml],
DE [auth t4],
TA [auth ml],
XD [auth T4]		IPR055122Mediator complex subunit MED14, N-terminalDomain
DD [auth Ml],
DE [auth t4],
TA [auth ml],
XD [auth T4]		IPR013947Mediator complex, subunit Med14Family
CD [auth Mk],
SA [auth mk]		IPR019145Mediator complex, subunit Med10Family
BD [auth Mj],
RA [auth mj]		IPR011425Mediator of RNA polymerase II transcription subunit 9Family
AD [auth Mi],
QA [auth mi]		IPR037212Mediator complex, subunit Med7/Med21-likeHomologous Superfamily
AD [auth Mi],
QA [auth mi]		IPR009244Mediator complex, subunit Med7Family
AD [auth Mi],
QA [auth mi]		IPR044888Mediator complex, subunit Med7 superfmailyHomologous Superfamily
PA [auth mh],
ZC [auth Mh]		IPR019258Mediator complex, subunit Med4Family
OA [auth mg],
YC [auth Mg]		IPR009332Mediator of RNA polymerase II transcription subunit 22Family
OA [auth mg],
YC [auth Mg]		IPR016530Mediator of RNA polymerase II transcription subunit 22, SaccharomycetesFamily
D [auth B3],
NB [auth A3]		IPR017907Zinc finger, RING-type, conserved siteConserved Site
D [auth B3],
NB [auth A3]		IPR004575Cdk-activating kinase assembly factor MAT1/Tfb3Family
D [auth B3],
NB [auth A3]		IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
D [auth B3],
NB [auth A3]		IPR015877MAT1, centreDomain
D [auth B3],
NB [auth A3]		IPR001841Zinc finger, RING-typeDomain
NA [auth mf],
XC [auth Mf]		IPR013921Mediator complex, subunit Med20Family
NA [auth mf],
XC [auth Mf]		IPR016532Mediator of RNA polymerase II transcription subunit 20Family
MA [auth me],
WC [auth Me]		IPR019095Mediator complex, subunit Med18Family
LA [auth md],
VC [auth Md]		IPR063477Mediator complex subunit 17, N-terminal domainDomain
LA [auth md],
VC [auth Md]		IPR019313Mediator complex, subunit Med17Family
KA [auth mc],
UC [auth Mc]		IPR019404Mediator complex, subunit Med11Family
JA [auth mb],
TC [auth Mb]		IPR019364Mediator complex, subunit Med8, fungi/metazoaFamily
IA [auth ma],
SC [auth Ma]		IPR007018Mediator complex, subunit Med6Family
IA [auth ma],
SC [auth Ma]		IPR016612Mediator complex, subunit Med6, fungiFamily
IA [auth ma],
SC [auth Ma]		IPR038566Mediator complex, subunit Med6 superfamilyHomologous Superfamily
GA [auth BX],
QC [auth AX]		IPR040501TFA2, Winged helix domain 2Domain
GA [auth BX],
QC [auth AX]		IPR054600Transcription initiation factor IIE subunit beta, E-tetherDomain
GA [auth BX],
QC [auth AX]		IPR016656Transcription initiation factor TFIIE, beta subunitFamily
GA [auth BX],
QC [auth AX]		IPR003166Transcription factor TFIIE beta subunit, DNA-binding domainDomain
FA [auth BW],
PC [auth AW]		IPR024550TFIIEalpha/SarR/Rpc3 HTH domainDomain
FA [auth BW],
PC [auth AW]		IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
FA [auth BW],
PC [auth AW]		IPR039997Transcription factor EFamily
FA [auth BW],
PC [auth AW]		IPR017919Transcription factor TFE/TFIIEalpha HTH domainDomain
FA [auth BW],
PC [auth AW]		IPR002853Transcription initiation factor IIE subunit alpha, N-terminalDomain
EA [auth BV],
OC [auth AV]		IPR015871Transcription initiation factor IIA, gamma subunit, C-terminalDomain
EA [auth BV],
OC [auth AV]		IPR015872Transcription initiation factor IIA, gamma subunit, N-terminalDomain
EA [auth BV],
OC [auth AV]		IPR009083Transcription factor IIA, alpha-helical domainHomologous Superfamily
EA [auth BV],
OC [auth AV]		IPR009088Transcription factor IIA, beta-barrelHomologous Superfamily
EA [auth BV],
OC [auth AV]		IPR003194Transcription initiation factor IIA, gamma subunitFamily
DA [auth BU],
NC [auth AU]		IPR004855Transcription factor IIA, alpha/beta subunitFamily
DA [auth BU],
NC [auth AU]		IPR009088Transcription factor IIA, beta-barrelHomologous Superfamily
C [auth B2],
MB [auth A2]		IPR040662Transcription factor Tfb2, C-terminal domainDomain
C [auth B2],
MB [auth A2]		IPR004598Transcription factor TFIIH subunit p52/Tfb2Family
BA [auth BS],
LC [auth AS]		IPR006289Transcription elongation factor, TFIISFamily
BA [auth BS],
LC [auth AS]		IPR001222Zinc finger, TFIIS-typeDomain
BA [auth BS],
LC [auth AS]		IPR003618Transcription elongation factor S-II, central domainDomain
BA [auth BS],
LC [auth AS]		IPR035441TFIIS/LEDGF domain superfamilyHomologous Superfamily
BA [auth BS],
LC [auth AS]		IPR036575Transcription elongation factor S-II, central domain superfamilyHomologous Superfamily
BA [auth BS],
LC [auth AS]		IPR035100Transcription elongation factor, IIS-typeFamily
BA [auth BS],
LC [auth AS]		IPR017923Transcription factor IIS, N-terminalDomain
BA [auth BS],
LC [auth AS]		IPR003617Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-typeDomain
AA [auth BR],
KC [auth AR]		IPR003196Transcription initiation factor IIF, beta subunitFamily
AA [auth BR],
KC [auth AR]		IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
AA [auth BR],
KC [auth AR]		IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
AA [auth BR],
KC [auth AR]		IPR040450TFIIF beta subunit, HTH domainDomain
AA [auth BR],
KC [auth AR]		IPR040504TFIIF, beta subunit, N-terminalDomain
AA [auth BR],
KC [auth AR]		IPR011039Transcription Factor IIF, Rap30/Rap74, interactionHomologous Superfamily
JC [auth AQ],
Z [auth BQ]		IPR008851Transcription initiation factor IIF, alpha subunitFamily
JC [auth AQ],
Z [auth BQ]		IPR011039Transcription Factor IIF, Rap30/Rap74, interactionHomologous Superfamily
IC [auth AO],
Y [auth BO]		IPR030491TATA-box binding protein, conserved siteConserved Site
IC [auth AO],
Y [auth BO]		IPR000814TATA-box binding proteinFamily
IC [auth AO],
Y [auth BO]		IPR012295TBP domain superfamilyHomologous Superfamily
IC [auth AO],
Y [auth BO]		IPR033710TATA-box binding protein, eukaryoticFamily
GC [auth AM],
W [auth BM]		IPR000812Transcription factor TFIIBFamily
GC [auth AM],
W [auth BM]		IPR023486Transcription factor TFIIB, conserved siteConserved Site
GC [auth AM],
W [auth BM]		IPR013150Transcription factor TFIIB, cyclin-like domainDomain
GC [auth AM],
W [auth BM]		IPR013137Zinc finger, TFIIB-typeDomain
GC [auth AM],
W [auth BM]		IPR036915Cyclin-like superfamilyHomologous Superfamily
GC [auth AM],
W [auth BM]		IPR013763Cyclin-like domainDomain
FC [auth AL],
V [auth BL]		IPR039747RPABC4Unknown
FC [auth AL],
V [auth BL]		IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4Family
FC [auth AL],
V [auth BL]		IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
EC [auth AK],
U [auth BK]		IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
EC [auth AK],
U [auth BK]		IPR037685RNA polymerase RBP11Family
EC [auth AK],
U [auth BK]		IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
EC [auth AK],
U [auth BK]		IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
EC [auth AK],
U [auth BK]		IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
DC [auth AJ],
T [auth BJ]		IPR023580RNA polymerase subunit RPB10Homologous Superfamily
DC [auth AJ],
T [auth BJ]		IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
DC [auth AJ],
T [auth BJ]		IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
B [auth B1],
LB [auth A1]		IPR013876TFIIH p62 subunit, N-terminalDomain
B [auth B1],
LB [auth A1]		IPR035925BSD domain superfamilyHomologous Superfamily
B [auth B1],
LB [auth A1]		IPR027079TFIIH subunit Tfb1/GTF2H1Family
B [auth B1],
LB [auth A1]		IPR011993PH-like domain superfamilyHomologous Superfamily
B [auth B1],
LB [auth A1]		IPR005607BSD domainDomain
CC [auth AI],
S [auth BI]		IPR001529DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbonDomain
CC [auth AI],
S [auth BI]		IPR012164DNA-directed RNA polymerase subunit/transcription factor SFamily
CC [auth AI],
S [auth BI]		IPR001222Zinc finger, TFIIS-typeDomain
CC [auth AI],
S [auth BI]		IPR034012Pol II subunit B9, C-terminal zinc ribbonDomain
CC [auth AI],
S [auth BI]		IPR019761DNA-directed RNA polymerase M, 15kDa subunit, conserved siteConserved Site
BC [auth AH],
R [auth BH]		IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
BC [auth AH],
R [auth BH]		IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
AC [auth AG],
Q [auth BG]		IPR003029S1 domainDomain
AC [auth AG],
Q [auth BG]		IPR045113RNA polymerase subunit Rpb7-likeFamily
AC [auth AG],
Q [auth BG]		IPR005576RNA polymerase Rpb7-like , N-terminalDomain
AC [auth AG],
Q [auth BG]		IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
AC [auth AG],
Q [auth BG]		IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
P [auth BF],
ZB [auth AF]		IPR028363DNA-directed RNA polymerase, subunit RPB6Family
P [auth BF],
ZB [auth AF]		IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily
P [auth BF],
ZB [auth AF]		IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
P [auth BF],
ZB [auth AF]		IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
P [auth BF],
ZB [auth AF]		IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
O [auth BE],
YB [auth AE]		IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
O [auth BE],
YB [auth AE]		IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
O [auth BE],
YB [auth AE]		IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
O [auth BE],
YB [auth AE]		IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
O [auth BE],
YB [auth AE]		IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
O [auth BE],
YB [auth AE]		IPR005571RNA polymerase, Rpb5, N-terminalDomain
N [auth BD],
XB [auth AD]		IPR005574RNA polymerase subunit Rpb4/RPC9Family
N [auth BD],
XB [auth AD]		IPR010997HRDC-like superfamilyHomologous Superfamily
N [auth BD],
XB [auth AD]		IPR006590RNA polymerase Rpb4/RPC9, coreDomain
N [auth BD],
XB [auth AD]		IPR038324Rpb4/RPC9 superfamilyHomologous Superfamily
N [auth BD],
XB [auth AD]		IPR045222DNA-directed RNA polymerase II subunit Rpb4-likeFamily
M [auth BC],
WB [auth AC]		IPR011262DNA-directed RNA polymerase, insert domainDomain
M [auth BC],
WB [auth AC]		IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
M [auth BC],
WB [auth AC]		IPR022842DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1Family
M [auth BC],
WB [auth AC]		IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
M [auth BC],
WB [auth AC]		IPR001514DNA-directed RNA polymerase, 30-40kDa subunit, conserved siteConserved Site
M [auth BC],
WB [auth AC]		IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
L [auth BB],
VB [auth AB]		IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
L [auth BB],
VB [auth AB]		IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
L [auth BB],
VB [auth AB]		IPR007646RNA polymerase Rpb2, domain 4Domain
L [auth BB],
VB [auth AB]		IPR007647RNA polymerase Rpb2, domain 5Domain
L [auth BB],
VB [auth AB]		IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
L [auth BB],
VB [auth AB]		IPR007642RNA polymerase Rpb2, domain 2Domain
L [auth BB],
VB [auth AB]		IPR015712DNA-directed RNA polymerase, subunit 2Family
L [auth BB],
VB [auth AB]		IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
L [auth BB],
VB [auth AB]		IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
L [auth BB],
VB [auth AB]		IPR007645RNA polymerase Rpb2, domain 3Domain
L [auth BB],
VB [auth AB]		IPR007644RNA polymerase, beta subunit, protrusionDomain
L [auth BB],
VB [auth AB]		IPR007641RNA polymerase Rpb2, domain 7Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR007081RNA polymerase Rpb1, domain 5Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR007075RNA polymerase Rpb1, domain 6Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR000684RNA polymerase II, heptapeptide repeat, eukaryoticRepeat
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR007083RNA polymerase Rpb1, domain 4Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR006592RNA polymerase, N-terminalDomain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR007066RNA polymerase Rpb1, domain 3Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR007073RNA polymerase Rpb1, domain 7Domain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR038593RNA polymerase Rpb1, domain 7 superfamilyHomologous Superfamily
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR000722RNA polymerase, alpha subunitDomain
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
HA [auth mA],
K [auth BA],
RC [auth MA],
UB [auth AA]		IPR007080RNA polymerase Rpb1, domain 1Domain
J [auth B9],
TB [auth A9]		IPR027353NET domainDomain
J [auth B9],
TB [auth A9]		IPR016665SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14Family
J [auth B9],
TB [auth A9]		IPR038704YEATS superfamilyHomologous Superfamily
J [auth B9],
TB [auth A9]		IPR005033YEATSFamily
J [auth B9],
TB [auth A9]		IPR055129YEATS domainDomain
A [auth B0],
KB [auth A0]		IPR010643Helical and beta-bridge domainDomain
A [auth B0],
KB [auth A0]		IPR045028Helicase superfamily 1/2, DinG/Rad3-likeFamily
A [auth B0],
KB [auth A0]		IPR002464DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved siteConserved Site
A [auth B0],
KB [auth A0]		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
A [auth B0],
KB [auth A0]		IPR042493Bacterial type XPD DNA helicase, FeS cluster domainHomologous Superfamily
A [auth B0],
KB [auth A0]		IPR006554Helicase-like, DEXD box c2 typeDomain
A [auth B0],
KB [auth A0]		IPR006555ATP-dependent helicase, C-terminalDomain
A [auth B0],
KB [auth A0]		IPR010614RAD3-like helicase, DEADDomain
A [auth B0],
KB [auth A0]		IPR014013Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-typeDomain
A [auth B0],
KB [auth A0]		IPR001945RAD3/XPDFamily
A [auth B0],
KB [auth A0]		IPR013020ATP-dependent helicase Rad3/Chl1-likeFamily