7AY1

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


This is version 2.0 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: 10.1038/s41594-021-00576-8
  • Primary Citation of 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 ...

    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.


    Related Citations: 
    • Structural basis of FANCD2 deubiquitination by USP1-UAF1
      Rennie, M.L., Arkinson, C., Chaugule, V.K., Toth, R., Walden, H.
      (2020) Biorxiv --: --

    Organizational Affiliation

    MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK. Helen.Walden@glasgow.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fanconi anemia group I proteinA1335Homo sapiensMutation(s): 0 
Gene Names: FANCIKIAA1794
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Find proteins for Q9NVI1 (Homo sapiens)
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Go to UniProtKB:  Q9NVI1
PHAROS:  Q9NVI1
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UniProt GroupQ9NVI1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fanconi anemia group D2 proteinB1455Homo sapiensMutation(s): 0 
Gene Names: FANCD2FACD
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Find proteins for Q9BXW9 (Homo sapiens)
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Go to UniProtKB:  Q9BXW9
PHAROS:  Q9BXW9
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UniProt GroupQ9BXW9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40C80Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
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Find proteins for P62987 (Homo sapiens)
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PHAROS:  P62987
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UniProt GroupP62987
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 1D786Homo sapiensMutation(s): 3 
Gene Names: USP1
EC: 3.4.19.12
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Find proteins for O94782 (Homo sapiens)
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PHAROS:  O94782
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UniProt GroupO94782
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 48E694Homo sapiensMutation(s): 0 
Gene Names: WDR48KIAA1449UAF1
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Find proteins for Q8TAF3 (Homo sapiens)
Explore Q8TAF3 
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PHAROS:  Q8TAF3
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UniProt GroupQ8TAF3
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (61-MER)F [auth S],
G [auth T]
29synthetic construct
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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, Database references, Polymer sequence, Source and taxonomy, Structure summary