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- EMDB-38232: The cryo-EM structure of the RAD51 L2 loop bound to the linker DN... -

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Basic information

Entry
Database: EMDB / ID: EMD-38232
TitleThe cryo-EM structure of the RAD51 L2 loop bound to the linker DNA with the blunt end of the nucleosome
Map data
Sample
  • Complex: RAD51-nucleosome complex
    • DNA: DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3')
    • DNA: DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3')
    • Protein or peptide: DNA repair protein RAD51 homolog 1
KeywordsNucleosome / Recombinase / DNA BINDING PROTEIN-DNA Complex
Function / homology
Function and homology information


presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / telomere maintenance via telomere lengthening / : / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex ...presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / telomere maintenance via telomere lengthening / : / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / DNA strand invasion / cellular response to hydroxyurea / mitotic recombination / lateral element / DNA strand exchange activity / replication-born double-strand break repair via sister chromatid exchange / Impaired BRCA2 binding to PALB2 / telomere maintenance via recombination / regulation of DNA damage checkpoint / single-stranded DNA helicase activity / reciprocal meiotic recombination / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / ATP-dependent DNA damage sensor activity / Impaired BRCA2 binding to RAD51 / regulation of double-strand break repair via homologous recombination / nuclear chromosome / replication fork processing / Transcriptional Regulation by E2F6 / : / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / response to X-ray / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / male germ cell nucleus / condensed nuclear chromosome / meiotic cell cycle / cellular response to ionizing radiation / cellular response to gamma radiation / double-strand break repair via homologous recombination / PML body / HDR through Homologous Recombination (HRR) / Meiotic recombination / response to toxic substance / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / DNA recombination / chromosome, telomeric region / mitochondrial matrix / response to xenobiotic stimulus / DNA repair / centrosome / DNA damage response / chromatin binding / nucleolus / chromatin / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.36 Å
AuthorsShioi T / Hatazawa S / Ogasawara M / Takizawa Y / Kurumizaka H
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22K06098 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121009 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Society for the Promotion of Science (JSPS)JP23K14134 Japan
CitationJournal: Nature / Year: 2024
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
DepositionDec 7, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38232.png

Downloads & links

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Map

FileDownload / File: emd_38232.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0056901635 - 0.021600556
Average (Standard dev.)0.000067807385 (±0.0005271247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38232_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_38232_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : RAD51-nucleosome complex

EntireName: RAD51-nucleosome complex
Components
  • Complex: RAD51-nucleosome complex
    • DNA: DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3')
    • DNA: DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3')
    • Protein or peptide: DNA repair protein RAD51 homolog 1

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Supramolecule #1: RAD51-nucleosome complex

SupramoleculeName: RAD51-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP...

MacromoleculeName: DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3')
type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 48.595086 KDa
SequenceString: (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)(DC)(DG)

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Macromolecule #2: DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP...

MacromoleculeName: DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.952062 KDa
SequenceString: (DC)(DG)(DT)(DG)(DG)(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) ...String:
(DC)(DG)(DT)(DG)(DG)(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)

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Macromolecule #3: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.291398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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: DNA repair protein RAD51 homolog 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5nwl


Details: 5Y0C and 7OHC were also used.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42054
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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