Crystal structure of the human Dmc1 protein

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.294 
  • R-Value Observed: 0.295 

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Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein dmc1

Kinebuchi, T.Kagawa, W.Enomoto, R.Tanaka, K.Miyagawa, K.Shibata, T.Kurumizaka, H.Yokoyama, S.

(2004) Mol Cell 14: 363-374

  • DOI: https://doi.org/10.1016/s1097-2765(04)00218-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The human Dmc1 protein, a RecA/Rad51 homolog, is a meiosis-specific DNA recombinase that catalyzes homologous pairing. RecA and Rad51 form helical filaments, while Dmc1 forms an octameric ring. In the present study, we crystallized the full-length human Dmc1 protein and solved the structure of the Dmc1 octameric ring. The monomeric structure of the Dmc1 protein closely resembled those of the human and archaeal Rad51 proteins. In addition to the polymerization motif that was previously identified in the Rad51 proteins, we found another hydrogen bonding interaction at the polymer interface, which could explain why Dmc1 forms stable octameric rings instead of helical filaments. Mutagenesis studies identified the inner and outer basic patches that are important for homologous pairing. The inner patch binds both single-stranded and double-stranded DNAs, while the outer one binds single-stranded DNA. Based on these results, we propose a model for the interaction of the Dmc1 rings with DNA.

  • Organizational Affiliation

    Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.294 
  • R-Value Observed: 0.295 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.091α = 90
b = 124.091β = 90
c = 218.83γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description