7ZWC

Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II.

Rengachari, S.Schilbach, S.Kaliyappan, T.Gouge, J.Zumer, K.Schwarz, J.Urlaub, H.Dienemann, C.Vannini, A.Cramer, P.

(2022) Nat Struct Mol Biol 29: 1159-1169

  • DOI: https://doi.org/10.1038/s41594-022-00857-w
  • Primary Citation of Related Structures:  
    7ZWC, 7ZWD, 7ZX7, 7ZX8, 7ZXE

  • PubMed Abstract: 

    RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes, such as small nuclear RNA (snRNA) genes, is less well understood at the structural level. Here, we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol IIpre-initiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE), located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc, called wing-1 and wing-2, bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBA [auth M]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q00403 (Homo sapiens)
Explore Q00403 
Go to UniProtKB:  Q00403
GTEx:  ENSG00000137947 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00403
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinB [auth O]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
UniProt & NIH Common Fund Data Resources
Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
GTEx:  ENSG00000112592 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20226
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1C [auth U]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
UniProt & NIH Common Fund Data Resources
Find proteins for P52655 (Homo sapiens)
Explore P52655 
Go to UniProtKB:  P52655
PHAROS:  P52655
GTEx:  ENSG00000165417 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52655
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2D [auth V]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
UniProt & NIH Common Fund Data Resources
Find proteins for P52657 (Homo sapiens)
Explore P52657 
Go to UniProtKB:  P52657
PHAROS:  P52657
GTEx:  ENSG00000140307 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52657
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
snRNA-activating protein complex subunit 1E [auth a]368Homo sapiensMutation(s): 0 
Gene Names: SNAPC1SNAP43
UniProt & NIH Common Fund Data Resources
Find proteins for Q16533 (Homo sapiens)
Explore Q16533 
Go to UniProtKB:  Q16533
PHAROS:  Q16533
GTEx:  ENSG00000023608 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16533
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
snRNA-activating protein complex subunit 3F [auth b]411Homo sapiensMutation(s): 0 
Gene Names: SNAPC3SNAP50
UniProt & NIH Common Fund Data Resources
Find proteins for Q92966 (Homo sapiens)
Explore Q92966 
Go to UniProtKB:  Q92966
PHAROS:  Q92966
GTEx:  ENSG00000164975 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92966
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
snRNA-activating protein complex subunit 4G [auth c]1,469Homo sapiensMutation(s): 0 
Gene Names: SNAPC4SNAP190
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SXM2 (Homo sapiens)
Explore Q5SXM2 
Go to UniProtKB:  Q5SXM2
PHAROS:  Q5SXM2
GTEx:  ENSG00000165684 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SXM2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
snRNA-activating protein complex subunit 5H [auth d]98Homo sapiensMutation(s): 0 
Gene Names: SNAPC5SNAP19
UniProt & NIH Common Fund Data Resources
Find proteins for O75971 (Homo sapiens)
Explore O75971 
Go to UniProtKB:  O75971
PHAROS:  O75971
GTEx:  ENSG00000174446 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75971
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains LengthOrganismImage
Non-template strandI [auth N]96Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains LengthOrganismImage
Template strandJ [auth T]96Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanyEXC 2067/1 39072994
Cancer Research UKUnited KingdomCR-UK C47547/A21536
Wellcome TrustUnited Kingdom200818/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2022-12-28
    Changes: Database references