- EMDB-29695: CryoEM structure of yeast recombination mediator Rad52 -
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Basic information
Entry
Database: EMDB / ID: EMD-29695
Title
CryoEM structure of yeast recombination mediator Rad52
Map data
Sample
Complex: Rad52 decamer
Protein or peptide: DNA repair and recombination protein RAD52
Keywords
Recombination mediator protein / DNA repair / Apo structure / Decamer / RECOMBINATION
Function / homology
Function and homology information
HDR through Single Strand Annealing (SSA) / meiotic joint molecule formation / double-strand break repair via single-strand annealing / DNA amplification / DNA/DNA annealing activity / SUMOylation of DNA damage response and repair proteins / DNA recombinase assembly / telomere maintenance via recombination / mitotic recombination / DNA strand exchange activity ...HDR through Single Strand Annealing (SSA) / meiotic joint molecule formation / double-strand break repair via single-strand annealing / DNA amplification / DNA/DNA annealing activity / SUMOylation of DNA damage response and repair proteins / DNA recombinase assembly / telomere maintenance via recombination / mitotic recombination / DNA strand exchange activity / double-strand break repair via break-induced replication / postreplication repair / nuclear chromosome / mitochondrial DNA repair / double-strand break repair via homologous recombination / mitochondrion / nucleus Similarity search - Function
DNA recombination/repair protein Rad52 / DNA repair protein Rad52/59/22 / Rad52 family / DNA repair protein Rad52/59/22 superfamily / Rad52/22 family double-strand break repair protein Similarity search - Domain/homology
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM133967, GM130746
United States
Citation
Journal: Nat Commun / Year: 2023 Title: Yeast Rad52 is a homodecamer and possesses BRCA2-like bipartite Rad51 binding modes. Authors: Jaigeeth Deveryshetty / Rahul Chadda / Jenna R Mattice / Simrithaa Karunakaran / Michael J Rau / Katherine Basore / Nilisha Pokhrel / Noah Englander / James A J Fitzpatrick / Brian Bothner / Edwin Antony / 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 ...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.
Initial model was built de novo in ModelAngelo tool. the best-looking subunit was real space refined in Phenix, followed by manual building in Coot. Later C10 symmetry was applied, and real space refined in Phenix.
Refinement
Space: REAL / Protocol: AB INITIO MODEL
Output model
PDB-8g3g: CryoEM structure of yeast recombination mediator Rad52
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