6VAF

Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DNA clamp function of the monoubiquitinated Fanconi anaemia ID complex.

Wang, R.Wang, S.Dhar, A.Peralta, C.Pavletich, N.P.

(2020) Nature 580: 278-282

  • DOI: 10.1038/s41586-020-2110-6
  • Primary Citation of Related Structures:  
    6VAA, 6VAD, 6VAF, 6VAE

  • PubMed Abstract: 
  • The ID complex, involving the proteins FANCI and FANCD2, is required for the repair of DNA interstrand crosslinks (ICL) and related lesions 1 . These proteins are mutated in Fanconi anaemia, a disease in which patients are predisposed to c ...

    The ID complex, involving the proteins FANCI and FANCD2, is required for the repair of DNA interstrand crosslinks (ICL) and related lesions 1 . These proteins are mutated in Fanconi anaemia, a disease in which patients are predisposed to cancer. The Fanconi anaemia pathway of ICL repair is activated when a replication fork stalls at an ICL 2 ; this triggers monoubiquitination of the ID complex, in which one ubiquitin molecule is conjugated to each of FANCI and FANCD2. Monoubiquitination of ID is essential for ICL repair by excision, translesion synthesis and homologous recombination; however, its function remains unknown 1,3 . Here we report a cryo-electron microscopy structure of the monoubiquitinated human ID complex bound to DNA, and reveal that it forms a closed ring that encircles the DNA. By comparison with the structure of the non-ubiquitinated ID complex bound to ICL DNA-which we also report here-we show that monoubiquitination triggers a complete rearrangement of the open, trough-like ID structure through the ubiquitin of one protomer binding to the other protomer in a reciprocal fashion. These structures-together with biochemical data-indicate that the monoubiquitinated ID complex loses its preference for ICL and related branched DNA structures, and becomes a sliding DNA clamp that can coordinate the subsequent repair reactions. Our findings also reveal how monoubiquitination in general can induce an alternative protein structure with a new function.


    Organizational Affiliation

    Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. pavletin@mskcc.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fanconi anemia, complementation group IA1328Homo sapiensMutation(s): 0 
Gene Names: FANCIKIAA1794
Find proteins for Q9NVI1 (Homo sapiens)
Explore Q9NVI1 
Go to UniProtKB:  Q9NVI1
NIH Common Fund Data Resources
PHAROS  Q9NVI1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fanconi anemia group D2 proteinB1451Homo sapiensMutation(s): 0 
Gene Names: FANCD2FACD
Find proteins for Q9BXW9 (Homo sapiens)
Explore Q9BXW9 
Go to UniProtKB:  Q9BXW9
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PHAROS  Q9BXW9
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinD76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
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PHAROS  P0CG48
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (29-MER)S29Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (29-MER)T29Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-12-17 
  • Released Date: 2020-03-18 
  • Deposition Author(s): Pavletich, N.P.

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references