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- EMDB-38231: The cryo-EM structure of the RAD51 N-terminal lobe domain bound t... -
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Open data
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Basic information
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Title | The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome | ||||||||||||||||||
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Function / homology | ![]() presynaptic intermediate filament cytoskeleton / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / positive regulation of DNA ligation / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to hydroxyurea / replication-born double-strand break repair via sister chromatid exchange ...presynaptic intermediate filament cytoskeleton / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / positive regulation of DNA ligation / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to hydroxyurea / replication-born double-strand break repair via sister chromatid exchange / lateral element / telomere maintenance via recombination / DNA recombinase assembly / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||
![]() | Shioi T / Hatazawa S / Ogasawara M / Takizawa Y / Kurumizaka H | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Authors: Takuro Shioi / Suguru Hatazawa / Eriko Oya / Noriko Hosoya / Wataru Kobayashi / Mitsuo Ogasawara / Takehiko Kobayashi / Yoshimasa Takizawa / Hitoshi Kurumizaka / ![]() 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. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 97.5 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 80.6 MB 80.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xbwMC ![]() 8jndC ![]() 8jneC ![]() 8jnfC ![]() 8xbtC ![]() 8xbuC ![]() 8xbvC ![]() 8xbxC ![]() 8xbyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38231_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38231_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : RAD51-nucleosome complex
Entire | Name: RAD51-nucleosome complex |
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Components |
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-Supramolecule #1: RAD51-nucleosome complex
Supramolecule | Name: RAD51-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.719445 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA UniProtKB: ![]() |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.676703 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG UniProtKB: ![]() |
-Macromolecule #5: DNA repair protein RAD51 homolog 1
Macromolecule | Name: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 37.291398 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GSHMAMQMQL EANADTSVEE ESFGPQPISR LEQCGINAND VKKLEEAGFH TVEAVAYAPK KELINIKGIS EAKADKILAE AAKLVPMGF TTATEFHQRR SEIIQITTGS KELDKLLQGG IETGSITEMF GEFRTGKTQI CHTLAVTCQL PIDRGGGEGK A MYIDTEGT ...String: GSHMAMQMQL EANADTSVEE ESFGPQPISR LEQCGINAND VKKLEEAGFH TVEAVAYAPK KELINIKGIS EAKADKILAE AAKLVPMGF TTATEFHQRR SEIIQITTGS KELDKLLQGG IETGSITEMF GEFRTGKTQI CHTLAVTCQL PIDRGGGEGK A MYIDTEGT FRPERLLAVA ERYGLSGSDV LDNVAYARAF NTDHQTQLLY QASAMMVESR YALLIVDSAT ALYRTDYSGR GE LSARQMH LARFLRMLLR LADEFGVAVV ITNQVVAQVD GAAMFAADPK KPIGGNIIAH ASTTRLYLRK GRGETRICKI YDS PCLPEA EAMFAINADG VGDAKD UniProtKB: ![]() |
-Macromolecule #3: DNA (5'-D(P*AP*CP*CP*GP*CP*TP*TP*AP*AP*AP*CP*GP*CP*AP*CP*GP*TP*A)-3')
Macromolecule | Name: DNA (5'-D(P*AP*CP*CP*GP*CP*TP*TP*AP*AP*AP*CP*GP*CP*AP*CP*GP*TP*A)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 47.976699 KDa |
Sequence | String: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DA)(DC)(DC)(DC)(DA)(DA)(DG)(DA)(DC) (DA)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DA)(DG)(DA)(DC)(DA)(DG)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DC)(DA) (DA)(DC)(DG) (DA)(DA)(DA)(DA)(DC)(DG)(DG)(DC)(DC)(DA) (DC)(DC)(DA) |
-Macromolecule #4: DNA (5'-D(P*TP*AP*CP*GP*TP*GP*CP*GP*TP*TP*TP*AP*AP*GP*CP*GP*GP*T)-3')
Macromolecule | Name: DNA (5'-D(P*TP*AP*CP*GP*TP*GP*CP*GP*TP*TP*TP*AP*AP*GP*CP*GP*GP*T)-3') type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 47.37107 KDa |
Sequence | String: (DT)(DG)(DG)(DC)(DC)(DG)(DT)(DT)(DT)(DT) (DC)(DG)(DT)(DT)(DG)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DC)(DT)(DG)(DT)(DC)(DT)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DT)(DG) (DT) (DC)(DT)(DT)(DG)(DG)(DG) ...String: (DT)(DG)(DG)(DC)(DC)(DG)(DT)(DT)(DT)(DT) (DC)(DG)(DT)(DT)(DG)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DC)(DT)(DG)(DT)(DC)(DT)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DT)(DG) (DT) (DC)(DT)(DT)(DG)(DG)(DG)(DT)(DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT) (DG)(DG) (DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA) (DG)(DC)(DG)(DC)(DG)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT) (DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC)(DG)(DA) (DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DT)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG) (DG)(DG)(DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT) |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |