8QH5 | pdb_00008qh5

CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2023-09-06 Released: 2024-08-14 
  • Deposition Author(s): Lee, S.-H., Sixma, T.K.
  • Funding Organization(s): Netherlands Organisation for Scientific Research (NWO), European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The small CRL4 CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics.

Llerena Schiffmacher, D.A.Lee, S.H.Kliza, K.W.Theil, A.F.Akita, M.Helfricht, A.Bezstarosti, K.Gonzalo-Hansen, C.van Attikum, H.Verlaan-de Vries, M.Vertegaal, A.C.O.Hoeijmakers, J.H.J.Marteijn, J.A.Lans, H.Demmers, J.A.A.Vermeulen, M.Sixma, T.K.Ogi, T.Vermeulen, W.Pines, A.

(2024) Nat Commun 15: 6374-6374

  • DOI: https://doi.org/10.1038/s41467-024-50584-7
  • Primary Citation of Related Structures:  
    8QH5

  • PubMed Abstract: 

    Transcription-blocking DNA lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional output and thereby cellular homeostasis to counteract aging. TC-NER is initiated by the stalling of RNA polymerase II at DNA lesions, which triggers the assembly of the TC-NER-specific proteins CSA, CSB and UVSSA. CSA, a WD40-repeat containing protein, is the substrate receptor subunit of a cullin-RING ubiquitin ligase complex composed of DDB1, CUL4A/B and RBX1 (CRL4 CSA ). Although ubiquitination of several TC-NER proteins by CRL4 CSA has been reported, it is still unknown how this complex is regulated. To unravel the dynamic molecular interactions and the regulation of this complex, we apply a single-step protein-complex isolation coupled to mass spectrometry analysis and identified DDA1 as a CSA interacting protein. Cryo-EM analysis shows that DDA1 is an integral component of the CRL4 CSA complex. Functional analysis reveals that DDA1 coordinates ubiquitination dynamics during TC-NER and is required for efficient turnover and progression of this process.


  • Organizational Affiliation
    • Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UV-stimulated scaffold protein AA [auth D]729Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-8B [auth A]408Homo 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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1C [auth B]1,160Homo 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
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1D [auth C]152Homo sapiensMutation(s): 0 
Gene Names: DDA1C19orf58PCIA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW61 (Homo sapiens)
Explore Q9BW61 
Go to UniProtKB:  Q9BW61
PHAROS:  Q9BW61
GTEx:  ENSG00000130311 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BW61
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.3.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)NetherlandsTOP 714.017.003
European Molecular Biology Organization (EMBO)European UnionALTF 1159-2019

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references, Structure summary