7ZF1 | pdb_00007zf1

Structure of ubiquitinated FANCI in complex with FANCD2 and double-stranded DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZF1

This is version 1.3 of the entry. See complete history

Literature

Structural and biochemical basis of interdependent FANCI-FANCD2 ubiquitination.

Lemonidis, K.Rennie, M.L.Arkinson, C.Chaugule, V.K.Clarke, M.Streetley, J.Walden, H.

(2023) EMBO J 42: e111898-e111898

  • DOI: https://doi.org/10.15252/embj.2022111898
  • Primary Citation Related Structures: 
    7ZF1

  • PubMed Abstract: 

    Di-monoubiquitination of the FANCI-FANCD2 (ID2) complex is a central and crucial step for the repair of DNA interstrand crosslinks via the Fanconi anaemia pathway. While FANCD2 ubiquitination precedes FANCI ubiquitination, FANCD2 is also deubiquitinated at a faster rate than FANCI, which can result in a FANCI-ubiquitinated ID2 complex (I Ub D2). Here, we present a 4.1 Å cryo-EM structure of I Ub D2 complex bound to double-stranded DNA. We show that this complex, like ID2 Ub and I Ub D2 Ub , is also in the closed ID2 conformation and clamps on DNA. The target lysine of FANCD2 (K561) becomes fully exposed in the I Ub D2-DNA structure and is thus primed for ubiquitination. Similarly, FANCI's target lysine (K523) is also primed for ubiquitination in the ID2 Ub -DNA complex. The I Ub D2-DNA complex exhibits deubiquitination resistance, conferred by the presence of DNA and FANCD2. ID2 Ub -DNA, on the other hand, can be efficiently deubiquitinated by USP1-UAF1, unless further ubiquitination on FANCI occurs. Therefore, FANCI ubiquitination effectively maintains FANCD2 ubiquitination in two ways: it prevents excessive FANCD2 deubiquitination within an I Ub D2 Ub -DNA complex, and it enables re-ubiquitination of FANCD2 within a transient, closed-on-DNA, I Ub D2 complex.


  • Organizational Affiliation
    • School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.

Macromolecule Content 

  • Total Structure Weight: 345.68 kDa 
  • Atom Count: 19,458 
  • Modeled Residue Count: 2,351 
  • Deposited Residue Count: 2,961 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fanconi anemia group I protein1,355Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVI1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fanconi anemia group D2 protein1,468Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXW9
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Reference Sequence
Find similar proteins by:|  3D Structure
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62987
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (61-MER)D [auth S]29synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (61-MER)E [auth T]29synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.14 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)European UnionERC- 2015-CoG-681582 ICLUb

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2023-02-08
    Changes: Database references, Refinement description
  • Version 1.3: 2024-07-24
    Changes: Data collection, Refinement description