9FSP | pdb_00009fsp

RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into distinct mechanisms of RNA polymerase II and III recruitment to snRNA promoters.

Shah, S.Z.Perry, T.N.Graziadei, A.Cecatiello, V.Kaliyappan, T.Misiaszek, A.D.Muller, C.W.Ramsay, E.P.Vannini, A.

(2025) Nat Commun 16: 141-141

  • DOI: https://doi.org/10.1038/s41467-024-55553-8
  • Primary Citation of Related Structures:  
    9A8W, 9FSO, 9FSP, 9FSQ, 9FSR, 9FSS

  • PubMed Abstract: 

    RNA polymerase III (Pol III) transcribes short, essential RNAs, including the U6 small nuclear RNA (snRNA). At U6 snRNA genes, Pol III is recruited by the snRNA Activating Protein Complex (SNAPc) and a Brf2-containing TFIIIB complex, forming a pre-initiation complex (PIC). Uniquely, SNAPc also recruits Pol II at the remaining splicesosomal snRNA genes (U1, 2, 4 and 5). The mechanism of SNAPc cross-polymerase engagement and the role of the SNAPC2 and SNAPC5 subunits remain poorly defined. Here, we present cryo-EM structures of the full-length SNAPc-containing Pol III PIC assembled on the U6 snRNA promoter in the open and melting states at 3.2-4.2 Å resolution. The structural comparison revealed differences with the Saccharomyces cerevisiae Pol III PIC and the basis of selective SNAPc engagement within Pol III and Pol II PICs. Additionally, crosslinking mass spectrometry localizes SNAPC2 and SNAPC5 near the promoter DNA, expanding upon existing descriptions of snRNA Pol III PIC structure.


  • Organizational Affiliation
    • Human Technopole, Milan, Italy.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC11,390Homo sapiensMutation(s): 0 
EC: 2.7.7.6
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PHAROS:  O14802
GTEx:  ENSG00000148606 
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UniProt GroupO14802
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC21,133Homo sapiensMutation(s): 0 
EC: 2.7.7.6
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PHAROS:  Q9NW08
GTEx:  ENSG00000013503 
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UniProt GroupQ9NW08
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC3534Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186141 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC4398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168495 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC5708Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000058600 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC6316Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132664 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC7223Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113356 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC8204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100413 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC9148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241258 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC10108Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161980 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1346Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171453 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC2133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186184 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1210Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099817 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100142 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163882 
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UniProt GroupP52434
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC458Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147669 
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UniProt GroupP53803
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177700 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding protein200Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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GTEx:  ENSG00000112592 
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UniProt GroupP20226
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor IIIB 50 kDa subunit419Homo sapiensMutation(s): 0 
Gene Names: BRF2BRFUPRO1470
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GTEx:  ENSG00000104221 
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UniProt GroupQ9HAW0
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor TFIIIB component B'' homolog484Homo sapiensMutation(s): 0 
Gene Names: BDP1KIAA1241KIAA1689TFNR
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PHAROS:  A6H8Y1
GTEx:  ENSG00000145734 
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UniProt GroupA6H8Y1
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
snRNA-activating protein complex subunit 1368Homo sapiensMutation(s): 0 
Gene Names: SNAPC1SNAP43
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GTEx:  ENSG00000023608 
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UniProt GroupQ16533
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
snRNA-activating protein complex subunit 4V [auth W]1,519Homo sapiensMutation(s): 0 
Gene Names: SNAPC4SNAP190
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PHAROS:  Q5SXM2
GTEx:  ENSG00000165684 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
snRNA-activating protein complex subunit 3Y [auth Z]411Homo sapiensMutation(s): 0 
Gene Names: SNAPC3SNAP50
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GTEx:  ENSG00000164975 
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Entity ID: 23
MoleculeChains LengthOrganismImage
U6_2_TemplateW [auth X]98Homo sapiens
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Entity ID: 24
MoleculeChains LengthOrganismImage
U6_2_Non templateX [auth Y]98Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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DA [auth F]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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AA [auth A]
CA [auth B]
EA [auth J]
FA [auth P]
GA [auth Q]
AA [auth A],
CA [auth B],
EA [auth J],
FA [auth P],
GA [auth Q],
HA [auth S],
IA [auth Z],
JA [auth Z],
Z [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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BA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.3.1
MODEL REFINEMENTPHENIXdev_5246

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release