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	Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Journal, issue, pages	Nature, Vol. 628, Issue 8006, Page 212-220, Year 2024
Publish date	Mar 20, 2024
Authors	Takuro Shioi / Suguru Hatazawa / Eriko Oya / Noriko Hosoya / Wataru Kobayashi / Mitsuo Ogasawara / Takehiko Kobayashi / Yoshimasa Takizawa / Hitoshi Kurumizaka /
PubMed Abstract	RAD51 is the central eukaryotic recombinase required for meiotic recombination and mitotic repair of double-strand DNA breaks (DSBs). However, the mechanism by which RAD51 functions at DSB sites in ...RAD51 is the central eukaryotic recombinase required for meiotic recombination and mitotic repair of double-strand DNA breaks (DSBs). However, the mechanism by which RAD51 functions at DSB sites in chromatin has remained elusive. Here we report the cryo-electron microscopy structures of human RAD51-nucleosome complexes, in which RAD51 forms ring and filament conformations. In the ring forms, the N-terminal lobe domains (NLDs) of RAD51 protomers are aligned on the outside of the RAD51 ring, and directly bind to the nucleosomal DNA. The nucleosomal linker DNA that contains the DSB site is recognized by the L1 and L2 loops-active centres that face the central hole of the RAD51 ring. In the filament form, the nucleosomal DNA is peeled by the RAD51 filament extension, and the NLDs of RAD51 protomers proximal to the nucleosome bind to the remaining nucleosomal DNA and histones. Mutations that affect nucleosome-binding residues of the RAD51 NLD decrease nucleosome binding, but barely affect DNA binding in vitro. Consistently, yeast Rad51 mutants with the corresponding mutations are substantially defective in DNA repair in vivo. These results reveal an unexpected function of the RAD51 NLD, and explain the mechanism by which RAD51 associates with nucleosomes, recognizes DSBs and forms the active filament in chromatin.
External links	Nature / PubMed:38509361 / PubMed Central
Methods	EM (single particle)
Resolution	2.89 - 7.8 Å
Structure data	36442 8jnd EMDB-36442, PDB-8jnd: The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Method: EM (single particle) / Resolution: 3.66 Å 36443 8jne EMDB-36443, PDB-8jne: The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Method: EM (single particle) / Resolution: 4.68 Å 36444 8jnf EMDB-36444, PDB-8jnf: The cryo-EM structure of the RAD51 filament bound to the nucleosome Method: EM (single particle) / Resolution: 6.91 Å 38228 8xbt EMDB-38228, PDB-8xbt: The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Method: EM (single particle) / Resolution: 4.12 Å 38229 8xbu EMDB-38229, PDB-8xbu: The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Method: EM (single particle) / Resolution: 4.24 Å 38230 8xbv EMDB-38230, PDB-8xbv: The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the sticky end of the nucleosome Method: EM (single particle) / Resolution: 7.61 Å 38231 8xbw EMDB-38231, PDB-8xbw: The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome Method: EM (single particle) / Resolution: 2.89 Å 38232 8xbx EMDB-38232, PDB-8xbx: The cryo-EM structure of the RAD51 L2 loop bound to the linker DNA with the blunt end of the nucleosome Method: EM (single particle) / Resolution: 4.36 Å 38233 8xby EMDB-38233, PDB-8xby: The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the blunt end of the nucleosome Method: EM (single particle) / Resolution: 7.8 Å
Source	homo sapiens (human) synthetic construct (others) escherichia coli (E. coli)
Keywords	DNA BINDING PROTEIN/DNA / Nucleosome / Recombinase / DNA BINDING PROTEIN-DNA Complex