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- EMDB-44104: Yeast Rad51-ssDNA filament -

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Basic information

Entry
Database: EMDB / ID: EMD-44104
TitleYeast Rad51-ssDNA filament
Map dataMap of yeast Rad51-ssDNA filament bound to ADP-AlF3
Sample
  • Complex: yeast Rad51 in complex with ssDNA and ADP-aluminium fluoride
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*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'-DIPHOSPHATE
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: MAGNESIUM ION
Keywordsgenome stability / recombination / Rad51 / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Presynaptic phase of homologous DNA pairing and strand exchange / heteroduplex formation / meiotic joint molecule formation / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / DNA strand invasion / mitotic recombination / DNA strand exchange activity ...Presynaptic phase of homologous DNA pairing and strand exchange / heteroduplex formation / meiotic joint molecule formation / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / DNA strand invasion / mitotic recombination / DNA strand exchange activity / telomere maintenance via recombination / reciprocal meiotic recombination / mitochondrial DNA repair / ATP-dependent DNA damage sensor activity / 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 / mitochondrial matrix / DNA binding / ATP binding / identical protein binding
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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLiu J / Gore S / Heyer W-D
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58015 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137751 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA093373 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129541 United States
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments.
Authors: Jie Liu / Steven K Gore / Wolf-Dietrich Heyer /
Abstract: Homologous recombination (HR) is a high-fidelity repair mechanism for double-strand breaks. Rad51 is the key enzyme that forms filaments on single-stranded DNA (ssDNA) to catalyze homology search and ...Homologous recombination (HR) is a high-fidelity repair mechanism for double-strand breaks. Rad51 is the key enzyme that forms filaments on single-stranded DNA (ssDNA) to catalyze homology search and DNA strand exchange in recombinational DNA repair. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) to ascertain the density map of the wild-type budding yeast Rad51-ssDNA filament bound to ADP-AlF3, achieving a resolution of 2.35 Å without imposing helical symmetry. The model assigned 6 Rad51 protomers, 24 nt of DNA, and 6 bound ADP-AlF3. It shows 6-fold symmetry implying monomeric building blocks, unlike the structure of the Rad51-I345T mutant filament with three-fold symmetry implying dimeric building blocks, for which the structural comparisons provide a satisfying mechanistic explanation. This image analysis enables comprehensive comparisons of individual Rad51 protomers within the filament and reveals local conformational movements of amino acid side chains. Notably, R293 in Loop 1 adopts multiple conformations to facilitate L296 and V331 in separating and twisting the DNA triplets. We also analyzed the crystal structure of Rad51-I345T and the predicted structure of yeast Rad51-K342E using the Rad51-ssDNA structure from this study as a reference.
History
DepositionMar 14, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44104.png

Downloads & links

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Map

FileDownload / File: emd_44104.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of yeast Rad51-ssDNA filament bound to ADP-AlF3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 448 pix.
= 304.64 Å		0.68 Å/pix.
x 448 pix.
= 304.64 Å		0.68 Å/pix.
x 448 pix.
= 304.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.188
Minimum - Maximum-1.1413175 - 2.9132745
Average (Standard dev.)0.00060619734 (±0.04037779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44104_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of yeast Rad51-ssDNA filament bound to ADP-AlF3

Fileemd_44104_half_map_1.map
AnnotationHalf map of yeast Rad51-ssDNA filament bound to ADP-AlF3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of yeast Rad51-ssDNA filament bound to ADP-AlF3

Fileemd_44104_half_map_2.map
AnnotationHalf map of yeast Rad51-ssDNA filament bound to ADP-AlF3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast Rad51 in complex with ssDNA and ADP-aluminium fluoride

EntireName: yeast Rad51 in complex with ssDNA and ADP-aluminium fluoride
Components
  • Complex: yeast Rad51 in complex with ssDNA and ADP-aluminium fluoride
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*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'-DIPHOSPHATE
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: yeast Rad51 in complex with ssDNA and ADP-aluminium fluoride

SupramoleculeName: yeast Rad51 in complex with ssDNA and ADP-aluminium fluoride
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 258 KDa

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Macromolecule #1: DNA repair protein RAD51

MacromoleculeName: DNA repair protein RAD51 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 43.007328 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSQVQEQHIS ESQLQYGNGS LMSTVPADLS QSVVDGNGNG SSEDIEATNG SGDGGGLQEQ AEAQGEMEDE AYDEAALGSF VPIEKLQVN GITMADVKKL RESGLHTAEA VAYAPRKDLL EIKGISEAKA DKLLNEAARL VPMGFVTAAD FHMRRSELIC L TTGSKNLD ...String:
MSQVQEQHIS ESQLQYGNGS LMSTVPADLS QSVVDGNGNG SSEDIEATNG SGDGGGLQEQ AEAQGEMEDE AYDEAALGSF VPIEKLQVN GITMADVKKL RESGLHTAEA VAYAPRKDLL EIKGISEAKA DKLLNEAARL VPMGFVTAAD FHMRRSELIC L TTGSKNLD TLLGGGVETG SITELFGEFR TGKSQLCHTL AVTCQIPLDI GGGEGKCLYI DTEGTFRPVR LVSIAQRFGL DP DDALNNV AYARAYNADH QLRLLDAAAQ MMSESRFSLI VVDSVMALYR TDFSGRGELS ARQMHLAKFM RALQRLADQF GVA VVVTNQ VVAQVDGGMA FNPDPKKPIG GNIMAHSSTT RLGFKKGKGC QRLCKVVDSP CLPEAECVFA IYEDGVGDPR EEDE

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*TP...

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*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: 7.25567 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 4 / Number of copies: 6 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / 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

Concentration0.65 mg/mL
BufferpH: 7.4
Details: 35 mM Tris-acetate pH 7.5, 7 mM magnesium acetate, 50 mM NaCl, 5% glycerol, 1 mM ADP-AlF3, and 1 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse filament particles.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1901160
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2) / Type: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1szp

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 1901160
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.2)

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Atomic model buiding 1

Initial modelPDB ID:

1szp


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 82.4
Output model

PDB-9b2d:
Yeast Rad51-ssDNA filament

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