9ED3

Yeast Rad51 in complex with ssDNA and ADP-aluminium fluoride

Summary for 9ED3

• Entry DOI: 10.2210/pdb9ed3/pdb
• Related: 9B2D
• EMDB information: 44104 44105
• Descriptor: DNA repair protein RAD51, DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: genome stability, recombination, rad51, dna repair, dna binding protein
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 7
• Total formula weight: 268512.54

Authors

Liu, J.,Gore, S.,Heyer, W.-D. (deposition date: 2024-11-15, release date: 2025-01-29, Last modification date: 2026-02-11)

Primary citation

Liu, J.,Gore, S.K.,Heyer, W.D.
Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Homologous recombination (HR) is a high-fidelity repair mechanism for double-strand breaks. Rad51 is the key enzyme that forms filaments on single-stranded DNA (ssDNA) to catalyze homology search and DNA strand exchange in recombinational DNA repair. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) to ascertain the density map of the wild-type budding yeast Rad51-ssDNA filament bound to ADP-AlF3, achieving a resolution of 2.35 Å without imposing helical symmetry. The model assigned 6 Rad51 protomers, 24 nt of DNA, and 6 bound ADP-AlF3. It shows 6-fold symmetry implying monomeric building blocks, unlike the structure of the Rad51-I345T mutant filament with three-fold symmetry implying dimeric building blocks, for which the structural comparisons provide a satisfying mechanistic explanation. This image analysis enables comprehensive comparisons of individual Rad51 protomers within the filament and reveals local conformational movements of amino acid side chains. Notably, R293 in Loop 1 adopts multiple conformations to facilitate L296 and V331 in separating and twisting the DNA triplets. We also analyzed the crystal structure of Rad51-I345T and the predicted structure of yeast Rad51-K342E using the Rad51-ssDNA structure from this study as a reference.

PubMed: 39898551
DOI: 10.1093/nar/gkaf052

Experimental method

ELECTRON MICROSCOPY (2.52 Å)