9YNH | pdb_00009ynh

Full-length human cytoplasmic dynein-1 in phi-like state bound to dynactin-p150glued and LIS1

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
N [auth P]SCOP2B SuperfamilyWD40 repeat-like 8103390 3001694 SCOP2B (2022-06-29)
M [auth O]SCOP2B SuperfamilyWD40 repeat-like 8103390 3001694 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyDLC-like 8051841 3000821 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyDLC-like 8051841 3000821 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyDLC-like 8034979 3000821 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyDLC-like 8034979 3000821 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRoadblock/LC7 domain-like 8033463 3001810 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyRoadblock/LC7 domain-like 8033463 3001810 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
Q [auth W],
R [auth X]		PF12455Dynein associated protein (Dynactin)Dynein associated protein- Family
M [auth O],
N [auth P]		PF24951PAC1 LisH domain (LisH_PAC1)PAC1 LisH domainThis entry represents a presumed LisH dimerisation domain found at the N-terminus of the PAC1 protein. PAC1 is the yeast homologue of the Lis1 protein. Domain
M [auth O],
N [auth P]		PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
K, L
PF03645Tctex-1 family (Tctex-1)Tctex-1 family- Family
I, J
PF01221Dynein light chain type 1 (Dynein_light)Dynein light chain type 1Domain
G, H
PF03259Roadblock/LC7 domain (Robl_LC7)Roadblock/LC7 domainThis family includes proteins that are about 100 amino acids long and have been shown to be related [3]. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is pro ...This family includes proteins that are about 100 amino acids long and have been shown to be related [3]. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions [2]. This family also includes Swiss:Q9Y2Q5 Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus Swiss:Q50883, a protein involved in gliding motility [4]. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.
Domain
C,
D,
O [auth U],
P [auth V]		PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
A, B
PF22597Dynein heavy chain, ATPase lid domain (DYN_lid)Dynein heavy chain, ATPase lid domainDyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport and comprise cytoplasmic and axonemal isoforms. They consist of a motor domain that contains a ring-shaped head ...Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport and comprise cytoplasmic and axonemal isoforms. They consist of a motor domain that contains a ring-shaped head with six AAA-domains, a coiled-coil stalk with a microtubule binding domain (MTBD) and a linker [1-5] This entry represents the lid domain found at the C-terminal of the third AAA+ ATPase domain in dyneins [1-5].
Domain
A, B
PF18198Dynein heavy chain AAA lid domain (AAA_lid_11)Dynein heavy chain AAA lid domainThis family represents the AAA lid domain found neat the C-terminal region of dynein heavy chain. Domain
A, B
PF12775P-loop containing dynein motor region (AAA_7)P-loop containing dynein motor regionThis domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliophathies. Dyneins share a conserved motor domain that couples cycles of ATP hydr ...This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliophathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs) [1].
Domain
A, B
PF12774Hydrolytic ATP binding site of dynein motor region (AAA_6)Hydrolytic ATP binding site of dynein motor regionThis domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydro ...This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities: AAA1-AAA6) [1]. This is the first site (out of four nucleotide binding sites in the dynein motor) where the movement depends on ATP hydrolysis [2]. When this site is nucleotide free or bound to ADP, the microtubule binding domain (MTBD) binds to the microtubule and the linker adopts the straight post-power-stroke conformation. Upon ATP binding and hydrolysis, the MTBD detaches from the microtubule and the linker is primed into the pre-power-stroke conformation. Dynein's AAA+ domains are each divided into an alpha/beta large subdomain designated with an L and and alpha small subdomains designated with an S. This is the AAA1 large (AAA1L) subdomain with the accompanying small subdomain (AAA1S). AAA1L, AAA1S and AAA2L enclose ADP.vanadate (ADP.Vi, ATP-hydrolysis transition state analogue). The AAA1L sensor-I loop, which varies in position depending on dynein's nucleotide state, swings in to contact AAA2L forming the important AAA1 nucleotide-binding site [1].
Domain
A, B
PF18199Dynein heavy chain C-terminal domain (Dynein_C)Dynein heavy chain C-terminal domainThis family represents the C-terminal domain of dynein heavy chain. This domain is a complex structure comprising six alpha-helices and an incomplete six-stranded antiparallel beta-barrel. The shape of this domain is distinctively flat, spreading ove ...This family represents the C-terminal domain of dynein heavy chain. This domain is a complex structure comprising six alpha-helices and an incomplete six-stranded antiparallel beta-barrel. The shape of this domain is distinctively flat, spreading over the AAA1, AAA5 and AAA6 domain [3].
Domain
A, B
PF12781ATP-binding dynein motor region (AAA_9)ATP-binding dynein motor regionThis domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydro ...This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the fifth AAA+ domain subdomain AAA5S. Structural analysis reveal that it is the coiled-coil buttress interface. The relative movement of AAA5S together with the stalk (AAA4S), is coupled to rearrangements in the AAA+ ring. Closure of the AAA1 site and the rigid body movement of AAA2-AAA4 force the AAA4/AAA5 interface to close and the AAA6L subdomain to rotate towards the ring centre. The AAA5S subdomain rotates as a unit together with AAA6L, and this movement pulls the buttress relative to the stalk [1].
Domain
A, B
PF08385Dynein heavy chain, N-terminal region 1 (DHC_N1)Dynein heavy chain, N-terminal region 1- Family
A, B
PF12780P-loop containing dynein motor region D4 (AAA_8)P-loop containing dynein motor region D4The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures describ ...The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor [1].
Domain
A, B
PF08393Dynein heavy chain, N-terminal region 2 (DHC_N2)Dynein heavy chain, N-terminal region 2- Family
A, B
PF17852Dynein heavy chain AAA lid domain (Dynein_AAA_lid)Dynein heavy chain AAA lid domainThis entry corresponds to the extension domain of AAA domain 5 in the dynein heavy chain [1]. This domain is composed of 8 alpha helices [1]. Domain
A, B
PF12777Microtubule-binding stalk of dynein motor (MT)Microtubule-binding stalk of dynein motorthe 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures describ ...the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [1].
Domain
A, B
PF03028Dynein heavy chain region D6 P-loop domain (Dynein_heavy)Dynein heavy chain region D6 P-loop domainThis family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved i ...This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains [1]. The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained [2].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Q [auth W],
R [auth X]		Dynactin subunit 1
M [auth O],
N [auth P]		Platelet-activating factor acetylhydrolase IB subunit beta
K, L
Dynein light chain Tctex-type 1
I, J
Dynein light chain 1, cytoplasmic
G, H
Dynein light chain roadblock-type 1
E, F
Cytoplasmic dynein 1 light intermediate chain 2
C,
D,
O [auth U],
P [auth V]		Cytoplasmic dynein 1 intermediate chain 2
A, B
Cytoplasmic dynein 1 heavy chain 1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
Q [auth W],
R [auth X]		IPR036859CAP Gly-rich domain superfamilyHomologous Superfamily
Q [auth W],
R [auth X]		IPR000938CAP Gly-rich domainDomain
Q [auth W],
R [auth X]		IPR022157Dynein associated proteinDomain
M [auth O],
N [auth P]		IPR019775WD40 repeat, conserved siteConserved Site
M [auth O],
N [auth P]		IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
M [auth O],
N [auth P]		IPR006594LIS1 homology motifConserved Site
M [auth O],
N [auth P]		IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
M [auth O],
N [auth P]		IPR037190LIS1, N-terminalHomologous Superfamily
M [auth O],
N [auth P]		IPR050349WD repeat LIS1/nudF dynein regulationFamily
M [auth O],
N [auth P]		IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
M [auth O],
N [auth P]		IPR056795PAC1-like, LisH-like dimerisation domainDomain
M [auth O],
N [auth P]		IPR001680WD40 repeatRepeat
M [auth O],
N [auth P]		IPR017252Dynein regulator LIS1Family
K, L
IPR038586Tctex-1-like superfamilyHomologous Superfamily
K, L
IPR005334Dynein light chain Tctex-1-likeFamily
I, J
IPR037177Dynein light chain superfamilyHomologous Superfamily
I, J
IPR019763Dynein light chain, type 1/2, conserved siteConserved Site
I, J
IPR001372Dynein light chain, type 1/2Family
G, H
IPR016561Dynein light chain roadblock-type 1/2Family
G, H
IPR004942Roadblock/LAMTOR2 domainDomain
E, F
IPR022780Dynein family light intermediate chainFamily
E, F
IPR008467Dynein 1 light intermediate chainFamily
E, F
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
C,
D,
O [auth U],
P [auth V]		IPR025956Cytoplasmic dynein 1 intermediate chain 1/2Family
C,
D,
O [auth U],
P [auth V]		IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
C,
D,
O [auth U],
P [auth V]		IPR001680WD40 repeatRepeat
C,
D,
O [auth U],
P [auth V]		IPR050687Dynein axonemal intermediate chain 1/2/3/4Family
C,
D,
O [auth U],
P [auth V]		IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
A, B
IPR026983Dynein heavy chainFamily
A, B
IPR013602Dynein heavy chain, linkerDomain
A, B
IPR041658Dynein heavy chain, AAA lid domainDomain
A, B
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
A, B
IPR042222Dynein heavy chain, domain 2, N-terminalHomologous Superfamily
A, B
IPR043160Dynein heavy chain, C-terminal domain, barrel regionHomologous Superfamily
A, B
IPR042219Dynein heavy chain, AAA lid domain superfamilyHomologous Superfamily
A, B
IPR035706Dynein heavy chain, ATP-binding dynein motor regionDomain
A, B
IPR041228Dynein heavy chain, C-terminal domainDomain
A, B
IPR054354Dynein 2 heavy chain 1, cytoplasmic, ATPase lid domainDomain
A, B
IPR003593AAA+ ATPase domainDomain
A, B
IPR041466Dynein heavy chain, AAA 5 extension domainDomain
A, B
IPR042228Dynein heavy chain, linker, subdomain 3Homologous Superfamily
A, B
IPR035699Dynein heavy chain, hydrolytic ATP-binding dynein motor regionDomain
A, B
IPR024743Dynein heavy chain, coiled coil stalkDomain
A, B
IPR013594Dynein heavy chain, tailDomain
A, B
IPR043157Dynein heavy chain, AAA1 domain, small subdomainHomologous Superfamily
A, B
IPR004273Dynein heavy chain, D6 P-loop domainDomain
A, B
IPR024317Dynein heavy chain, AAA module D4Domain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
Q [auth W],
R [auth X]		Pharos:  Q14203
M [auth O],
N [auth P]		Pharos:  P43034
K, L
Pharos:  P63172
I, J
Pharos:  P63167
G, H
Pharos:  Q9NP97
E, F
Pharos:  O43237
C,
D,
O [auth U],
P [auth V]		Pharos:  Q13409
A, B
Pharos:  Q14204