Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures.
Journal, issue, pages	Nature, Vol. 586, Issue 7831, Page 801-806, Year 2020
Publish date	Oct 14, 2020
Authors	Haijuan Yang / Chun Zhou / Ankita Dhar / Nikola P Pavletich /
PubMed Abstract	The strand-exchange reaction is central to homologous recombination. It is catalysed by the RecA family of ATPases, which form a helical filament with single-stranded DNA (ssDNA) and ATP. This ...The strand-exchange reaction is central to homologous recombination. It is catalysed by the RecA family of ATPases, which form a helical filament with single-stranded DNA (ssDNA) and ATP. This filament binds to a donor double-stranded DNA (dsDNA) to form synaptic filaments, which search for homology and then catalyse the exchange of the complementary strand, forming either a new heteroduplex or-if homology is limited-a D-loop. How synaptic filaments form, search for homology and catalyse strand exchange is poorly understood. Here we report the cryo-electron microscopy analysis of synaptic mini-filaments with both non-complementary and partially complementary dsDNA, and structures of RecA-D-loop complexes containing a 10- or a 12-base-pair heteroduplex. The C-terminal domain of RecA binds to dsDNA and directs it to the RecA L2 loop, which inserts into and opens up the duplex. The opening propagates through RecA sequestering the homologous strand at a secondary DNA-binding site, which frees the complementary strand to sample pairing with the ssDNA. At each RecA step, there is a roughly 20% probability that duplex opening will terminate and the as-yet-unopened dsDNA portion will bind to another C-terminal domain. Homology suppresses this process, through the cooperation of heteroduplex pairing with the binding of ssDNA to the secondary site, to extend dsDNA opening. This mechanism locally limits the length of ssDNA sampled for pairing if homology is not encountered, and could allow for the formation of multiple, widely separated synapses on the donor dsDNA, which would increase the likelihood of encountering homology. These findings provide key mechanistic insights into homologous recombination.
External links	Nature / PubMed:33057191 / PubMed Central
Methods	EM (single particle)
Resolution	2.4 - 2.9 Å
Structure data	22522 7jy6 EMDB-22522: Analysis of a strand exchange reaction with a mini filament of 9-RecA, oligo(dT)27 primary ssDNA, non-homologous 120 bp dsDNA and ATPgammaS. PDB-7jy6: Analysis of a strand exchange reaction with a mini filament of 9-RecA, oligo(dT)27 primary ssDNA, non-homologous 120 bp dsDNA and ATPgammaS Method: EM (single particle) / Resolution: 2.5 Å 22523 7jy7 EMDB-22523, PDB-7jy7: Structure of a 12 base pair RecA-D loop complex Method: EM (single particle) / Resolution: 2.9 Å 22524 7jy8 EMDB-22524: Analysis of a strand exchange reaction with a mini filament of 9-RecA, 27-mer ssDNA, partially-homologous 67 bp dsDNA and ATPgammaS. PDB-7jy8: Analysis of a strand exchange reaction with a mini filament of 9-RecA, 27-mer ssDNA, partially-homologous 67 bp dsDNA and ATPgammaS Method: EM (single particle) / Resolution: 2.4 Å 22525 7jy9 EMDB-22525: Structure of a 9 base pair RecA-D loop complex. PDB-7jy9: Structure of a 9 base pair RecA-D loop complex Method: EM (single particle) / Resolution: 2.7 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM
Source	escherichia coli (E. coli)
Keywords	DNA BINDING PROTEIN/DNA / Recombination / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex