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 8G3G | pdb_00008g3g

CryoEM structure of yeast recombination mediator Rad52


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8G3G

This is version 1.0 of the entry. See complete history. 

Literature

Yeast Rad52 is a homodecamer and possesses BRCA2-like bipartite Rad51 binding modes.

Deveryshetty, J., Chadda, R., Mattice, J.R., Karunakaran, S., Rau, M.J., Basore, K., Pokhrel, N., Englander, N., Fitzpatrick, J.A.J., Bothner, B., Antony, E.

(2023) Nat Commun 14: 6215-6215

  • DOI: https://doi.org/10.1038/s41467-023-41993-1
  • Primary Citation Related Structures: 
    8G3G

  • PubMed Abstract: 

    Homologous recombination (HR) is an essential double-stranded DNA break repair pathway. In HR, Rad52 facilitates the formation of Rad51 nucleoprotein filaments on RPA-coated ssDNA. Here, we decipher how Rad52 functions using single-particle cryo-electron microscopy and biophysical approaches. We report that Rad52 is a homodecameric ring and each subunit possesses an ordered N-terminal and disordered C-terminal half. An intrinsic structural asymmetry is observed where a few of the C-terminal halves interact with the ordered ring. We describe two conserved charged patches in the C-terminal half that harbor Rad51 and RPA interacting motifs. Interactions between these patches regulate ssDNA binding. Surprisingly, Rad51 interacts with Rad52 at two different bindings sites: one within the positive patch in the disordered C-terminus and the other in the ordered ring. We propose that these features drive Rad51 nucleation onto a single position on the DNA to promote formation of uniform pre-synaptic Rad51 filaments in HR.


  • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.

Macromolecule Content 

  • Total Structure Weight: 524.76 kDa 
  • Atom Count: 7,020 
  • Modeled Residue Count: 900 
  • Deposited Residue Count: 4,710 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair and recombination protein RAD52471Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD52, YML032C
UniProt
Find proteins for P06778 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06778 
Go to UniProtKB:  P06778
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06778
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2.0
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133967, GM130746

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release