2ZJB | pdb_00002zjb

Crystal structure of the human Dmc1-M200V polymorphic variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.351 (Depositor), 0.351 (DCC) 
  • R-Value Work: 
    0.294 (Depositor), 0.293 (DCC) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structural and functional analyses of the DMC1-M200V polymorphism found in the human population

Hikiba, J.Hirota, K.Kagawa, W.Ikawa, S.Kinebuchi, T.Sakane, I.Takizawa, Y.Yokoyama, S.Mandon-Pepin, B.Nicolas, A.Shibata, T.Ohta, K.Kurumizaka, H.

(2008) Nucleic Acids Res 36: 4181-4190

  • DOI: https://doi.org/10.1093/nar/gkn362
  • Primary Citation Related Structures: 
    2ZJB

  • PubMed Abstract: 

    The M200V polymorphism of the human DMC1 protein, which is an essential, meiosis-specific DNA recombinase, was found in an infertile patient, raising the question of whether this homozygous human DMC1-M200V polymorphism may cause infertility by affecting the function of the human DMC1 protein. In the present study, we determined the crystal structure of the human DMC1-M200V variant in the octameric-ring form. Biochemical analyses revealed that the human DMC1-M200V variant had reduced stability, and was moderately defective in catalyzing in vitro recombination reactions. The corresponding M194V mutation introduced in the Schizosaccharomyces pombe dmc1 gene caused a significant decrease in the meiotic homologous recombination frequency. Together, these structural, biochemical and genetic results provide extensive evidence that the human DMC1-M200V mutation impairs its function, supporting the previous interpretation that this single-nucleotide polymorphism is a source of human infertility.


  • Organizational Affiliation
    • Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

Macromolecule Content 

  • Total Structure Weight: 75.96 kDa 
  • Atom Count: 3,748 
  • Modeled Residue Count: 478 
  • Deposited Residue Count: 686 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Meiotic recombination protein DMC1/LIM15 homolog
A, B
343Homo sapiensMutation(s): 0 
Gene Names: DMC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14565 (Homo sapiens)
Explore Q14565 
Go to UniProtKB:  Q14565
PHAROS:  Q14565
GTEx:  ENSG00000100206 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14565
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.351 (Depositor), 0.351 (DCC) 
  • R-Value Work:  0.294 (Depositor), 0.293 (DCC) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.089α = 90
b = 124.089β = 90
c = 217.87γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description