9FFF

dsDNA-FANCD2-FANCI complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions.

Alcon, P.Kaczmarczyk, A.P.Ray, K.K.Liolios, T.Guilbaud, G.Sijacki, T.Shen, Y.McLaughlin, S.H.Sale, J.E.Knipscheer, P.Rueda, D.S.Passmore, L.A.

(2024) Nature 632: 1165-1173

  • DOI: https://doi.org/10.1038/s41586-024-07770-w
  • Primary Citation of Related Structures:  
    9FFB, 9FFF

  • PubMed Abstract: 

    DNA crosslinks block DNA replication and are repaired by the Fanconi anaemia pathway. The FANCD2-FANCI (D2-I) protein complex is central to this process as it initiates repair by coordinating DNA incisions around the lesion 1 . However, D2-I is also known to have a more general role in DNA repair and in protecting stalled replication forks from unscheduled degradation 2-4 . At present, it is unclear how DNA crosslinks are recognized and how D2-I functions in replication fork protection. Here, using single-molecule imaging, we show that D2-I is a sliding clamp that binds to and diffuses on double-stranded DNA. Notably, sliding D2-I stalls on encountering single-stranded-double-stranded (ss-ds) DNA junctions, structures that are generated when replication forks stall at DNA lesions 5 . Using cryogenic electron microscopy, we determined structures of D2-I on DNA that show that stalled D2-I makes specific interactions with the ss-dsDNA junction that are distinct from those made by sliding D2-I. Thus, D2-I surveys dsDNA and, when it reaches an ssDNA gap, it specifically clamps onto ss-dsDNA junctions. Because ss-dsDNA junctions are found at stalled replication forks, D2-I can identify sites of DNA damage. Therefore, our data provide a unified molecular mechanism that reconciles the roles of D2-I in the recognition and protection of stalled replication forks in several DNA repair pathways.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fanconi anemia protein FANCD21,475Gallus gallusMutation(s): 0 
Gene Names: fancd2
UniProt
Find proteins for Q68Y81 (Gallus gallus)
Explore Q68Y81 
Go to UniProtKB:  Q68Y81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68Y81
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fanconi anemia complementation group I1,338Gallus gallusMutation(s): 0 
Gene Names: FANCI
UniProt
Find proteins for B0I564 (Gallus gallus)
Explore B0I564 
Go to UniProtKB:  B0I564
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0I564
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (32-MER)C [auth S]32synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (33-MER)D [auth T]33synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomMC_U105192715

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-02
    Changes: Data collection, Database references