4M6W | pdb_00004m6w

Crystal structure of the C-terminal segment of FANCM in complex with FAAP24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.299 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.254 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4M6W

This is version 1.2 of the entry. See complete history

Literature

Structural insights into the functions of the FANCM-FAAP24 complex in DNA repair.

Yang, H.Zhang, T.Tao, Y.Wang, F.Tong, L.Ding, J.

(2013) Nucleic Acids Res 41: 10573-10583

  • DOI: https://doi.org/10.1093/nar/gkt788
  • Primary Citation Related Structures: 
    4M6W

  • PubMed Abstract: 

    Fanconi anemia (FA) is a genetically heterogeneous disorder associated with deficiencies in the FA complementation group network. FA complementation group M (FANCM) and FA-associated protein 24 kDa (FAAP24) form a stable complex to anchor the FA core complex to chromatin in repairing DNA interstrand crosslinks. Here, we report the first crystal structure of the C-terminal segment of FANCM in complex with FAAP24. The C-terminal segment of FANCM and FAAP24 both consist of a nuclease domain at the N-terminus and a tandem helix-hairpin-helix (HhH)2 domain at the C-terminus. The FANCM-FAAP24 complex exhibits a similar architecture as that of ApXPF. However, the variations of several key residues and the electrostatic property at the active-site region render a catalytically inactive nuclease domain of FANCM, accounting for the lack of nuclease activity. We also show that the first HhH motif of FAAP24 is a potential binding site for DNA, which plays a critical role in targeting FANCM-FAAP24 to chromatin. These results reveal the mechanistic insights into the functions of FANCM-FAAP24 in DNA repair.


  • Organizational Affiliation
    • State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, Graduate School of Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China and Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

Macromolecule Content 

  • Total Structure Weight: 48.82 kDa 
  • Atom Count: 3,081 
  • Modeled Residue Count: 388 
  • Deposited Residue Count: 429 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fanconi anemia group M protein221Homo sapiensMutation(s): 0 
Gene Names: FANCMKIAA1596
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYD8 (Homo sapiens)
Explore Q8IYD8 
Go to UniProtKB:  Q8IYD8
PHAROS:  Q8IYD8
GTEx:  ENSG00000187790 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IYD8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fanconi anemia-associated protein of 24 kDa208Homo sapiensMutation(s): 0 
Gene Names: FAAP24C19orf40
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BTP7 (Homo sapiens)
Explore Q9BTP7 
Go to UniProtKB:  Q9BTP7
PHAROS:  Q9BTP7
GTEx:  ENSG00000131944 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BTP7
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.299 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.254 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.174α = 90
b = 98.111β = 90
c = 140.156γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations