9D4N | pdb_00009d4n

The cryo-EM structure of the yeast Dmc1 filament bound to ssDNA in the presence of ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Lineage-specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases.

Petassi, M.Shin, Y.Jessop, A.M.Morse, K.Kim, S.Y.Kuppa, S.Matei, R.Raina, V.B.Greene, E.C.

(2026) J Biological Chem 302: 111019-111019

  • DOI: https://doi.org/10.1016/j.jbc.2025.111019
  • Primary Citation of Related Structures:  
    9D46, 9D4N

  • PubMed Abstract: 

    Most eukaryotes possess two Rad51/RecA family DNA recombinases that are thought to have arisen from an ancient gene duplication event: Rad51, which is expressed in both mitosis and meiosis; and Dmc1, which is only expressed in meiosis. To explore the evolutionary relationship between these recombinases, here, we present high-resolution cryo-EM structures of Saccharomyces cerevisiae Rad51 filaments and S. cerevisiae Dmc1 filaments bound to ssDNA, which reveal a pair of stacked interfacial aromatic amino acid residues that are nearly universally conserved in Rad51 but are absent from Dmc1. We use a combination of bioinformatics, genetic analysis of natural sequence variation, and deep mutational analysis to probe the functionally tolerated sequence space for these stacked aromatic residues. Our findings demonstrate that the functional landscape of the interfacial aromatic residues within the Rad51 filament is highly constrained. In contrast, the amino acids at the equivalent positions within the Dmc1 filament exhibit a broad functional landscape. This work helps highlight the distinct evolutionary trajectories of these two eukaryotic recombinases, which may have contributed to their functional and mechanistic divergence.


  • Organizational Affiliation
    • Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, New York, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meiotic recombination protein DMC1
A, B, C, D, E
A, B, C, D, E, F
334Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DMC1ISC2YER179W
UniProt
Find proteins for P25453 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25453 
Go to UniProtKB:  P25453
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25453
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')G [auth X]18Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
H [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
V [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
L [auth B]
N [auth C]
O [auth C]
I [auth A],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
T [auth E],
U [auth E],
W [auth F],
X [auth F],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF-MCB1817315

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 2.0: 2025-02-19
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Atomic model, Data collection, Data processing, Derived calculations, Structure summary
  • Version 2.1: 2026-02-11
    Changes: Data collection, Database references
  • Version 2.2: 2026-02-18
    Changes: Data collection, Database references