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- EMDB-47572: Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-47572
TitleCryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide
Map datastructure of yeast Rad51 nucleoprotein filament bound to Rad54peptide
Sample
  • Complex: Rad51 nucleoprotein filament bound to Rad54 peptide
    • Protein or peptide: DNA repair and recombination protein RAD54
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    • Protein or peptide: DNA repair protein RAD51
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsRad51 / DNA recombinase / Homologous recombination / DNA repair / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


double-strand break repair via synthesis-dependent strand annealing / Presynaptic phase of homologous DNA pairing and strand exchange / heteroduplex formation / meiotic joint molecule formation / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / mitochondrial chromosome / mitotic recombination-dependent replication fork processing ...double-strand break repair via synthesis-dependent strand annealing / Presynaptic phase of homologous DNA pairing and strand exchange / heteroduplex formation / meiotic joint molecule formation / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / DNA geometric change / DNA recombinase assembly / DNA strand invasion / mitotic recombination / DNA translocase activity / DNA strand exchange activity / DNA clamp loader activity / telomere maintenance via recombination / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / mitochondrial DNA repair / nuclear chromosome / ATP-dependent activity, acting on DNA / condensed nuclear chromosome / nucleotide-excision repair / double-strand break repair via homologous recombination / G2/M transition of mitotic cell cycle / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / mitochondrial matrix / chromatin remodeling / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Rad54, N-terminal / Rad54 N terminal / : / 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 ...Rad54, N-terminal / Rad54 N terminal / : / 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 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding 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 / DNA repair and recombination protein RAD54
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShin Y / Greene EC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide
Authors: Shin Y / Greene EC
History
DepositionOct 30, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47572.png

Downloads & links

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Map

FileDownload / File: emd_47572.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of yeast Rad51 nucleoprotein filament bound to Rad54peptide
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 216.064 Å		0.84 Å/pix.
x 256 pix.
= 216.064 Å		0.84 Å/pix.
x 256 pix.
= 216.064 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0076
Minimum - Maximum-0.12246577 - 0.30172116
Average (Standard dev.)0.0026919069 (±0.016628757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.064 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_47572_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_47572_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rad51 nucleoprotein filament bound to Rad54 peptide

EntireName: Rad51 nucleoprotein filament bound to Rad54 peptide
Components
  • Complex: Rad51 nucleoprotein filament bound to Rad54 peptide
    • Protein or peptide: DNA repair and recombination protein RAD54
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    • Protein or peptide: DNA repair protein RAD51
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Rad51 nucleoprotein filament bound to Rad54 peptide

SupramoleculeName: Rad51 nucleoprotein filament bound to Rad54 peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: DNA repair and recombination protein RAD54

MacromoleculeName: DNA repair and recombination protein RAD54 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 4.03373 KDa
SequenceString:
RRKDALSAQR LAKDPTRLSH IQYTLRRSFT VPIK

UniProtKB: DNA repair and recombination protein RAD54

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Macromolecule #3: DNA repair protein RAD51

MacromoleculeName: DNA repair protein RAD51 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.93007 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FVPIEKLQVN GITMADVKKL RESGLHTAEA VAYAPRKDLL EIKGISEAKA DKLLNEAARL VPMGFVTAAD FHMRRSELIC LTTGSKNLD TLLGGGVETG SITELFGEFR TGKSQLCHTL AVTCQIPLDI GGGEGKCLYI DTEGTFRPVR LVSIAQRFGL D PDDALNNV ...String:
FVPIEKLQVN GITMADVKKL RESGLHTAEA VAYAPRKDLL EIKGISEAKA DKLLNEAARL VPMGFVTAAD FHMRRSELIC LTTGSKNLD TLLGGGVETG SITELFGEFR TGKSQLCHTL AVTCQIPLDI GGGEGKCLYI DTEGTFRPVR LVSIAQRFGL D PDDALNNV AYARAYNADH QLRLLDAAAQ MMSESRFSLI VVDSVMALYR TDFSGRGELS ARQMHLAKFM RALQRLADQF GV AVVVTNQ VVAQVDGGMA FNPDPKKPIG GNIMAHSSTT RLGFKKGKGC QRLCKVVDSP CLPEAECVFA IYEDGVGDPR EED E

UniProtKB: DNA repair protein RAD51

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Macromolecule #2: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 5.430513 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 363379
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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