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


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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair and recombination protein RAD52471Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD52YML032C
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
Expand
  • 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