7C99

Human DMC1 post-synaptic complexes with mismatched dsDNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures.

Luo, S.C.Yeh, H.Y.Lan, W.H.Wu, Y.M.Yang, C.H.Chang, H.Y.Su, G.C.Lee, C.Y.Wu, W.J.Li, H.W.Ho, M.C.Chi, P.Tsai, M.D.

(2021) Nat Commun 12: 115-115

  • DOI: 10.1038/s41467-020-20258-1
  • Primary Citation of Related Structures:  
    7C9C, 7C9A, 7C98, 7C99, 7CGY

  • PubMed Abstract: 
  • Both high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1 ...

    Both high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open "triplet gate" for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases.


    Organizational Affiliation

    Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan. mdtsai@gate.sinica.edu.tw.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Meiotic recombination protein DMC1/LIM15 homologA, B, C340Homo sapiensMutation(s): 0 
Gene Names: DMC1DMC1HLIM15
UniProt & NIH Common Fund Data Resources
Find proteins for Q14565 (Homo sapiens)
Explore Q14565 
Go to UniProtKB:  Q14565
PHAROS:  Q14565
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')D9synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')E9synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ANP
      Query on ANP

      Download Ideal Coordinates CCD File 
      G [auth A], I [auth B], J [auth C]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
      C10 H17 N6 O12 P3
      PVKSNHVPLWYQGJ-KQYNXXCUSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      F [auth A], H [auth B], K [auth C]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 3.36 Å
      • Aggregation State: FILAMENT 
      • Reconstruction Method: HELICAL 

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Academia Sinica (Taiwan)TaiwanAS-KPQ-109-TPP2
      Academia Sinica (Taiwan)TaiwanAS-CFII-108-110
      Academia Sinica (Taiwan)TaiwanAS-KPQ-105-TPP

      Revision History  (Full details and data files)

      • Version 1.0: 2020-11-18
        Type: Initial release
      • Version 1.1: 2020-11-25
        Changes: Structure summary
      • Version 1.2: 2021-01-27
        Changes: Database references