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TitleLocal structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 3, Year 2025
Publish dateJan 24, 2025
AuthorsJie Liu / Steven K Gore / Wolf-Dietrich Heyer /
PubMed AbstractHomologous 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 ...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.
External linksNucleic Acids Res / PubMed:39898551 / PubMed Central
MethodsEM (single particle)
Resolution2.4 - 2.52 Å
Structure data

44104

9b2d

EMDB-44104, PDB-9b2d:
Yeast Rad51-ssDNA filament
Method: EM (single particle) / Resolution: 2.4 Å

PDB-9ed3:
Yeast Rad51 in complex with ssDNA and ADP-aluminium fluoride
Method: ELECTRON MICROSCOPY / Resolution: 2.52 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-AF3:
ALUMINUM FLUORIDE

ChemComp-MG:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae s288c (yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsDNA BINDING PROTEIN/DNA / genome stability / recombination / Rad51 / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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