7AY1 | pdb_00007ay1

Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and FANCI


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7AY1

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: 501.07 kDa 
  • Atom Count: 25,186 
  • Modeled Residue Count: 3,138 
  • Deposited Residue Count: 4,408 
  • Unique protein chains: 5
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fanconi anemia group I protein1,335Homo sapiensMutation(s): 0 
Gene Names: FANCIKIAA1794
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVI1 (Homo sapiens)
Explore Q9NVI1 
Go to UniProtKB:  Q9NVI1
PHAROS:  Q9NVI1
GTEx:  ENSG00000140525 
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UniProt GroupQ9NVI1
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fanconi anemia group D2 protein1,455Homo sapiensMutation(s): 0 
Gene Names: FANCD2FACD
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXW9 (Homo sapiens)
Explore Q9BXW9 
Go to UniProtKB:  Q9BXW9
PHAROS:  Q9BXW9
GTEx:  ENSG00000144554 
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UniProt GroupQ9BXW9
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L4080Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
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UniProt GroupP62987
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 1786Homo sapiensMutation(s): 3 
Gene Names: USP1
EC: 3.4.19.12
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Find proteins for O94782 (Homo sapiens)
Explore O94782 
Go to UniProtKB:  O94782
PHAROS:  O94782
GTEx:  ENSG00000162607 
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UniProt GroupO94782
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 48694Homo 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 
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UniProt GroupQ8TAF3
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (61-MER)F [auth S],
G [auth T]
29synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
H [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.13.2

Structure Validation

View Full Validation Report



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, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary