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- EMDB-47573: Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Hed1 -

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Basic information

Entry
Database: EMDB / ID: EMD-47573
TitleCryo-EM structure of yeast Rad51 nucleoprotein filament bound to Hed1
Map datastructure of yeast Rad51 nucleoprotein filament bound to Hed1
Sample
  • Complex: yeast Rad51 nucleoprotein filament bound to Hed1peptide
    • Protein or peptide: DNA repair protein RAD51
    • Protein or peptide: Meiosis-specific protein HED1
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsRad51 / Hed1 / DNA repair / Homologous recombination / Recombinase / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


negative regulation of DNA recombinase mediator complex assembly / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of mitotic recombination / heteroduplex formation / meiotic joint molecule formation / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / synaptonemal complex assembly ...negative regulation of DNA recombinase mediator complex assembly / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of mitotic recombination / heteroduplex formation / meiotic joint molecule formation / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / synaptonemal complex assembly / 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 / enzyme inhibitor activity / 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 repair / 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 / Meiosis-specific protein HED1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for Rad54- and Hed1-mediated regulation of Rad51 during the transition from mitotic to meiotic recombination.
Authors: Yeonoh Shin / Michael T Petassi / Aidan M Jessop / Stefan Y Kim / Razvan Matei / Katherine Morse / Vivek B Raina / Upasana Roy / Eric C Greene /
Abstract: Rad51 catalyzes the DNA pairing reactions that take place during homologous recombination (HR), and HR must be tightly regulated to ensure physiologically appropriate outcomes. Rad54 is an ATP- ...Rad51 catalyzes the DNA pairing reactions that take place during homologous recombination (HR), and HR must be tightly regulated to ensure physiologically appropriate outcomes. Rad54 is an ATP-dependent DNA motor protein that stimulates Rad51 activity during mitosis. In meiosis Rad51 is downregulated by the protein Hed1, which blocks Rad54 binding to Rad51, and allows Dmc1 to function as the active recombinase. We currently have a poor understanding of the regulatory interplay between Rad54, Hed1, Rad51, and Dmc1. Here, we identify a conserved Rad51 interaction motif within Rad54, and we solve a CryoEM structure of this motif bound to Rad51. We also identify a distinct Rad51 interaction motif within Hed1 and solve its structure bound to Rad51. These structures explain how Rad54 engages Rad51 to promote recombination between sister chromatids during mitosis and how Rad51 is downregulated by Hed1 upon entry into meiosis such that its meiosis-specific homolog Dmc1 can promote recombination between homologous chromosomes.
History
DepositionOct 30, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47573.png

Downloads & links

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Map

FileDownload / File: emd_47573.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of yeast Rad51 nucleoprotein filament bound to Hed1
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0944
Minimum - Maximum-0.3693424 - 0.93139887
Average (Standard dev.)0.0014659666 (±0.026545227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_47573_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_47573_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 : yeast Rad51 nucleoprotein filament bound to Hed1peptide

EntireName: yeast Rad51 nucleoprotein filament bound to Hed1peptide
Components
  • Complex: yeast Rad51 nucleoprotein filament bound to Hed1peptide
    • Protein or peptide: DNA repair protein RAD51
    • Protein or peptide: Meiosis-specific protein HED1
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: yeast Rad51 nucleoprotein filament bound to Hed1peptide

SupramoleculeName: yeast Rad51 nucleoprotein filament bound to Hed1peptide
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 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: 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: Meiosis-specific protein HED1

MacromoleculeName: Meiosis-specific protein HED1 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 3.931598 KDa
SequenceString:
KKSLKDLIYE TNKTFYQVDS NKVKYKVGLS KKQ

UniProtKB: Meiosis-specific protein HED1

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Macromolecule #3: 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: 3 / 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: 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.21 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 876496
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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