6FCV

Structure of the human DDB1-CSA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

TRiC controls transcription resumption after UV damage by regulating Cockayne syndrome protein A.

Pines, A.Dijk, M.Makowski, M.Meulenbroek, E.M.Vrouwe, M.G.van der Weegen, Y.Baltissen, M.French, P.J.van Royen, M.E.Luijsterburg, M.S.Mullenders, L.H.Vermeulen, M.Vermeulen, W.Pannu, N.S.van Attikum, H.

(2018) Nat Commun 9: 1040-1040

  • DOI: https://doi.org/10.1038/s41467-018-03484-6
  • Primary Citation of Related Structures:  
    6FCV

  • PubMed Abstract: 

    Transcription-blocking DNA lesions are removed by transcription-coupled nucleotide excision repair (TC-NER) to preserve cell viability. TC-NER is triggered by the stalling of RNA polymerase II at DNA lesions, leading to the recruitment of TC-NER-specific factors such as the CSA-DDB1-CUL4A-RBX1 cullin-RING ubiquitin ligase complex (CRL CSA ). Despite its vital role in TC-NER, little is known about the regulation of the CRL CSA complex during TC-NER. Using conventional and cross-linking immunoprecipitations coupled to mass spectrometry, we uncover a stable interaction between CSA and the TRiC chaperonin. TRiC's binding to CSA ensures its stability and DDB1-dependent assembly into the CRL CSA complex. Consequently, loss of TRiC leads to mislocalization and depletion of CSA, as well as impaired transcription recovery following UV damage, suggesting defects in TC-NER. Furthermore, Cockayne syndrome (CS)-causing mutations in CSA lead to increased TRiC binding and a failure to compose the CRL CSA complex. Thus, we uncover CSA as a TRiC substrate and reveal that TRiC regulates CSA-dependent TC-NER and the development of CS.


  • Organizational Affiliation

    Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 11,158Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-8416Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.79α = 90
b = 140.79β = 90
c = 249.331γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NWONetherlandsTOP Talent-021.002.024
NWONetherlandsVIDI-700.55.425

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description