7AY0 | pdb_00007ay0

Crystal structure of truncated USP1-UAF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.266 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7AY0

This is version 2.1 of the entry. See complete history

Literature

Structural basis of FANCD2 deubiquitination by USP1-UAF1.

Rennie, M.L.Arkinson, C.Chaugule, V.K.Toth, R.Walden, H.

(2021) Nat Struct Mol Biol 28: 356-364

  • DOI: https://doi.org/10.1038/s41594-021-00576-8
  • Primary Citation Related Structures: 
    7AY0, 7AY1, 7AY2

  • PubMed Abstract: 

    Ubiquitin-specific protease 1 (USP1) acts together with the cofactor UAF1 during DNA repair processes to specifically remove monoubiquitin signals. One substrate of the USP1-UAF1 complex is the monoubiquitinated FANCI-FANCD2 heterodimer, which is involved in the repair of DNA interstrand crosslinks via the Fanconi anemia pathway. Here we determine structures of human USP1-UAF1 with and without ubiquitin and bound to monoubiquitinated FANCI-FANCD2. The crystal structures of USP1-UAF1 reveal plasticity in USP1 and key differences to USP12-UAF1 and USP46-UAF1, two related proteases. A cryo-EM reconstruction of USP1-UAF1 in complex with monoubiquitinated FANCI-FANCD2 highlights a highly orchestrated deubiquitination process, with USP1-UAF1 driving conformational changes in the substrate. An extensive interface between UAF1 and FANCI, confirmed by mutagenesis and biochemical assays, provides a molecular explanation for the requirement of both proteins, despite neither being directly involved in catalysis. Overall, our data provide molecular details of USP1-UAF1 regulation and substrate recognition.


  • Organizational Affiliation
    • Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. Martin.Rennie@glasgow.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 216.82 kDa 
  • Atom Count: 12,749 
  • Modeled Residue Count: 1,610 
  • Deposited Residue Count: 1,920 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 48
A, C
563Homo sapiensMutation(s): 0 
Gene Names: WDR48KIAA1449UAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAF3 (Homo sapiens)
Explore Q8TAF3 
Go to UniProtKB:  Q8TAF3
PHAROS:  Q8TAF3
GTEx:  ENSG00000114742 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TAF3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 1
B, D
397Homo sapiensMutation(s): 0 
Gene Names: USP1
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O94782 (Homo sapiens)
Explore O94782 
Go to UniProtKB:  O94782
PHAROS:  O94782
GTEx:  ENSG00000162607 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94782
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.266 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.57α = 90
b = 119.57β = 90
c = 195.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United KingdomERC-2015-CoG-681582
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_12016/12

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2021-04-14
    Changes: Database references
  • Version 1.3: 2021-04-28
    Changes: Database references
  • Version 2.0: 2022-07-27
    Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description