8B3G

C(N)RL4CSA-UVSSA-E2-ubiquitin complex.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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 basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair.

Kokic, G.Yakoub, G.van den Heuvel, D.Wondergem, A.P.van der Meer, P.J.van der Weegen, Y.Chernev, A.Fianu, I.Fokkens, T.J.Lorenz, S.Urlaub, H.Cramer, P.Luijsterburg, M.S.

(2024) Nat Struct Mol Biol 31: 536-547

  • DOI: https://doi.org/10.1038/s41594-023-01207-0
  • Primary Citation of Related Structures:  
    8B3G

  • PubMed Abstract: 

    During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This transition requires site-specific ubiquitylation of Pol II by the CRL4 CSA ubiquitin ligase, a process that is facilitated by ELOF1 in an unknown way. Using cryogenic electron microscopy, biochemical assays and cell biology approaches, we found that ELOF1 serves as an adaptor to stably position UVSSA and CRL4 CSA on arrested Pol II, leading to ligase neddylation and activation of Pol II ubiquitylation. In the presence of ELOF1, a transcription factor IIS (TFIIS)-like element in UVSSA gets ordered and extends through the Pol II pore, thus preventing reactivation of Pol II by TFIIS. Our results provide the structural basis for Pol II ubiquitylation and inactivation in TCR.


  • 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
ubiquitin-conjugating enzyme E2 D2 isoform X3A [auth D]147Homo sapiensMutation(s): 0 
Gene Names: UBE2D2
UniProt
Find proteins for A0A6P5C4T4 (Bos indicus)
Explore A0A6P5C4T4 
Go to UniProtKB:  A0A6P5C4T4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6P5C4T4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NEDD8B [auth N]76Homo sapiensMutation(s): 0 
Gene Names: NEDD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q15843 (Homo sapiens)
Explore Q15843 
Go to UniProtKB:  Q15843
PHAROS:  Q15843
GTEx:  ENSG00000129559 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15843
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1C [auth R]108Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens)
Explore P62877 
Go to UniProtKB:  P62877
PHAROS:  P62877
GTEx:  ENSG00000100387 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62877
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinD [auth U]76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-8E [auth a]396Homo sapiensMutation(s): 0 
Gene Names: ERCC8CKN1CSA
UniProt & NIH Common Fund Data Resources
Find proteins for Q13216 (Homo sapiens)
Explore Q13216 
Go to UniProtKB:  Q13216
PHAROS:  Q13216
GTEx:  ENSG00000049167 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13216
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
UV-stimulated scaffold protein AF [auth c]709Homo sapiensMutation(s): 0 
Gene Names: UVSSAKIAA1530
UniProt & NIH Common Fund Data Resources
Find proteins for Q2YD98 (Homo sapiens)
Explore Q2YD98 
Go to UniProtKB:  Q2YD98
PHAROS:  Q2YD98
GTEx:  ENSG00000163945 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YD98
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1G [auth d]1,140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-4AH [auth e]759Homo sapiensMutation(s): 0 
Gene Names: CUL4A
UniProt & NIH Common Fund Data Resources
Find proteins for Q13619 (Homo sapiens)
Explore Q13619 
Go to UniProtKB:  Q13619
PHAROS:  Q13619
GTEx:  ENSG00000139842 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13619
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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)GermanyEXC 2067/1-390729940
European Research Council (ERC)European UnionAdvanced Investigator Grant CHROMATRANS (grant agreement No. 882357)

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release