9E6N | pdb_00009e6n

Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Hed1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for Rad54- and Hed1-mediated regulation of Rad51 during the transition from mitotic to meiotic recombination.

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

(2025) Proc Natl Acad Sci U S A 122: e2510007122-e2510007122

  • DOI: https://doi.org/10.1073/pnas.2510007122
  • Primary Citation of Related Structures:  
    9E6L, 9E6N

  • PubMed Abstract: 

    Rad51 catalyzes the DNA pairing reactions that take place during homologous recombination (HR), and HR must be tightly regulated to ensure physiologically appropriate outcomes. Rad54 is an ATP-dependent DNA motor protein that stimulates Rad51 activity during mitosis. In meiosis Rad51 is downregulated by the protein Hed1, which blocks Rad54 binding to Rad51, and allows Dmc1 to function as the active recombinase. We currently have a poor understanding of the regulatory interplay between Rad54, Hed1, Rad51, and Dmc1. Here, we identify a conserved Rad51 interaction motif within Rad54, and we solve a CryoEM structure of this motif bound to Rad51. We also identify a distinct Rad51 interaction motif within Hed1 and solve its structure bound to Rad51. These structures explain how Rad54 engages Rad51 to promote recombination between sister chromatids during mitosis and how Rad51 is downregulated by Hed1 upon entry into meiosis such that its meiosis-specific homolog Dmc1 can promote recombination between homologous chromosomes.


  • Organizational Affiliation
    • Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD51
A, B, C, D, E
A, B, C, D, E, F
321Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD51YER095W
UniProt
Find proteins for P25454 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25454 
Go to UniProtKB:  P25454
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25454
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Meiosis-specific protein HED1
G, H, I, J, K
33Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03937 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03937 
Go to UniProtKB:  Q03937
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03937
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
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')L [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 
M [auth A]
O [auth B]
Q [auth C]
S [auth D]
U [auth E]
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth A]
P [auth B]
R [auth C]
T [auth D]
V [auth E]
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.1_4122

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Data collection, Database references
  • Version 1.2: 2025-10-01
    Changes: Data collection, Database references