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TitleRAD51 D-loop structures reveal the mechanism of eukaryotic RAD51-mediated strand exchange.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Page 243, Year 2025
Publish dateDec 1, 2025
AuthorsShih-Chi Luo / Cheng-Han Yang / Hsin-Yi Yeh / Cheng-Wei Lin / Min-Chi Yeh / Peter Chi / Meng-Chiao Ho /
PubMed AbstractStrand exchange is a key step in homologous recombination, enabling template-based repair of DNA double-strand breaks. Eukaryotic RAD51 forms an ATP-dependent helical presynaptic filament on single- ...Strand exchange is a key step in homologous recombination, enabling template-based repair of DNA double-strand breaks. Eukaryotic RAD51 forms an ATP-dependent helical presynaptic filament on single-stranded DNA (ssDNA), which then searches for homologous double-stranded DNA (dsDNA), and catalyzes the strand exchange to form a D-loop in an ATP hydrolysis-independent manner. The molecular mechanism by which RAD51 facilitates dsDNA unwinding and pairing remains unclear. Here, we present cryo-EM structures of RAD51 mini-filaments bound to homologous dsDNA, capturing five intermediates from dsDNA recruitment to D-loop formation. These structures, together with molecular dynamics simulations, suggest a stepwise mechanism: the conserved N-terminal domain (NTD) recruits and bends the dsDNA, weakening base pairing near the exchange site. Subsequent engagement with positively-charged regions, including the loop L2 and loop Arg303-Arg306, further bends the homologous dsDNA, thereby not only positioning it closer to the strand exchange site but also inducing local base-pair opening. Additionally, the loop L2 (Met278 and Phe279) inserts between strands, and the secondary DNA binding sites (S2 sites) capture the displaced strand to prevent strand reannealing. Together, our findings provide detailed insight into a spatially coordinated mechanism of strand exchange by RAD51.
External linksNat Commun / PubMed:41326376 / PubMed Central
MethodsEM (single particle)
Resolution2.91 - 3.91 Å
Structure data

64183

9ui4

EMDB-64183, PDB-9ui4:
Rad51 presynaptic complex
Method: EM (single particle) / Resolution: 2.91 Å

64184

9ui5

EMDB-64184, PDB-9ui5:
Rad51 postsynaptic complex
Method: EM (single particle) / Resolution: 3.04 Å

64186

9ui7

EMDB-64186, PDB-9ui7:
structure of a 4 base pair Rad51 D-loop complex
Method: EM (single particle) / Resolution: 3.91 Å

64187

9ui8

EMDB-64187, PDB-9ui8:
structure of an 8 base pair Rad51 D-loop complex
Method: EM (single particle) / Resolution: 3.2 Å

64188

9ui9

EMDB-64188, PDB-9ui9:
structure of a 12 base pair Rad51 D-loop complex
Method: EM (single particle) / Resolution: 3.42 Å

EMDB-65955: structure of a 7 nucleotides homology Rad51 D-loop complex
Method: EM (single particle) / Resolution: 3.26 Å

Chemicals

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • mus musculus (house mouse)
KeywordsDNA BINDING PROTEIN/DNA / homologous recombination / strand exchange / D-loop / RECOMBINATION / DNA BINDING PROTEIN-DNA complex

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