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- EMDB-49485: The Cryo-EM structure of the yeast Rad51-ssDNA nucleoprotein fila... -

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Basic information

Entry
Database: EMDB / ID: EMD-49485
TitleThe Cryo-EM structure of the yeast Rad51-ssDNA nucleoprotein filament ADP bound state
Map datatructure of the yeast Rad51-ssDNA nucleoprotein filament ADP bound state
Sample
  • Complex: Cryo-EM structure of yeast Rad51 - ssDNA nucleoprotein filament ADP bound state
    • Protein or peptide: DNA repair protein RAD51
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsDNA Repair / Homologous Recombination / DNA BINDING PROTEIN
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 / double-strand break repair via homologous recombination / nucleotide-excision repair / G2/M transition of mitotic cell cycle / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / mitochondrial matrix / ATP hydrolysis activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsShin Y / Greene EC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-MCB1817315 United States
CitationJournal: J Biol Chem / Year: 2025
Title: ATP hydrolysis-driven structural transitions within the Saccharomyces cerevisiae Rad51 and Dmc1 nucleoprotein filaments.
Authors: Yeonoh Shin / Stefan Y Kim / Eric C Greene /
Abstract: Homologous recombination (HR) is essential for the maintenance of genome stability and for generating genetic diversity during meiosis. The eukaryotic protein Rad51 is member of the Rad51/RecA family ...Homologous recombination (HR) is essential for the maintenance of genome stability and for generating genetic diversity during meiosis. The eukaryotic protein Rad51 is member of the Rad51/RecA family of DNA recombinases and is responsible for guiding the DNA pairing reactions that take place in HR during mitosis. Dmc1 is a meiosis-specific paralog of Rad51 and is responsible for the DNA pairing reactions that take place in HR during meiosis. Rad51 and Dmc1 are both ATP-dependent DNA-binding proteins and both form extended helical filaments on ssDNA, which are key intermediates in HR. The stability of these nucleoprotein filaments is highly regulated and is also tightly coupled to nucleotide binding and hydrolysis. ATP binding promotes filament assembly, whereas the hydrolysis of ATP to ADP reduces filament stability to promote filament disassembly. Here, we present cryo-EM structures of the Saccharomyces cerevisiae recombinases Rad51 and Dmc1 in the ADP-bound states and provide a detailed structural comparison to the ATP-bound filaments. Our findings yield insights into the structural transitions that take place during the hydrolysis of ATP to ADP and suggest a new model for how these structural changes may be linked to nucleoprotein filament disassembly.
History
DepositionFeb 27, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49485.png

Downloads & links

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Map

FileDownload / File: emd_49485.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtructure of the yeast Rad51-ssDNA nucleoprotein filament ADP bound state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 307.8 Å		0.86 Å/pix.
x 360 pix.
= 307.8 Å		0.86 Å/pix.
x 360 pix.
= 307.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.052
Minimum - Maximum-0.27171806 - 0.4522558
Average (Standard dev.)0.0008781796 (±0.011951288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 307.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_49485_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49485_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of yeast Rad51 - ssDNA nucleoprotein filament A...

EntireName: Cryo-EM structure of yeast Rad51 - ssDNA nucleoprotein filament ADP bound state
Components
  • Complex: Cryo-EM structure of yeast Rad51 - ssDNA nucleoprotein filament ADP bound state
    • Protein or peptide: DNA repair protein RAD51
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of yeast Rad51 - ssDNA nucleoprotein filament A...

SupramoleculeName: Cryo-EM structure of yeast Rad51 - ssDNA nucleoprotein filament ADP bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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 (brewer's yeast)
Molecular weightTheoretical: 43.007328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / 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 #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / 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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 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: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 330601
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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