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- EMDB-46565: The cryo-EM structure of the yeast Dmc1 filament bound to ssDNA i... -

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Basic information

Entry
Database: EMDB / ID: EMD-46565
TitleThe cryo-EM structure of the yeast Dmc1 filament bound to ssDNA in the presence of ATP
Map dataStructure of the yeast Dmc1 filament bound to ssDNA in the presence of ATP
Sample
  • Complex: Cryo-EM structure of yeast Dmc1 filament bound on ssDNA in the presence of ATP
    • Protein or peptide: Meiotic recombination protein DMC1
    • 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
KeywordsDNA Repair / Homologous Recombination / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


meiotic joint molecule formation / synaptonemal complex assembly / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / DNA strand invasion / mitotic recombination / ATPase inhibitor activity / DNA strand exchange activity / reciprocal meiotic recombination / sporulation resulting in formation of a cellular spore ...meiotic joint molecule formation / synaptonemal complex assembly / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / DNA strand invasion / mitotic recombination / ATPase inhibitor activity / DNA strand exchange activity / reciprocal meiotic recombination / sporulation resulting in formation of a cellular spore / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / condensed nuclear chromosome / meiotic cell cycle / single-stranded DNA binding / double-stranded DNA binding / ATP binding / nucleus
Similarity search - Function
Meiotic recombination protein Dmc1 / 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 ...Meiotic recombination protein Dmc1 / 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
Meiotic recombination protein DMC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 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: 2026
Title: Lineage-specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases.
Authors: Mike Petassi / Yeonoh Shin / Aidan M Jessop / Katherine Morse / Stefan Y Kim / Sahiti Kuppa / Razvan Matei / Vivek B Raina / Eric C Greene /
Abstract: Most eukaryotes possess two Rad51/RecA family DNA recombinases that are thought to have arisen from an ancient gene duplication event: Rad51, which is expressed in both mitosis and meiosis; and Dmc1, ...Most eukaryotes possess two Rad51/RecA family DNA recombinases that are thought to have arisen from an ancient gene duplication event: Rad51, which is expressed in both mitosis and meiosis; and Dmc1, which is only expressed in meiosis. To explore the evolutionary relationship between these recombinases, here, we present high-resolution cryo-EM structures of Saccharomyces cerevisiae Rad51 filaments and S. cerevisiae Dmc1 filaments bound to ssDNA, which reveal a pair of stacked interfacial aromatic amino acid residues that are nearly universally conserved in Rad51 but are absent from Dmc1. We use a combination of bioinformatics, genetic analysis of natural sequence variation, and deep mutational analysis to probe the functionally tolerated sequence space for these stacked aromatic residues. Our findings demonstrate that the functional landscape of the interfacial aromatic residues within the Rad51 filament is highly constrained. In contrast, the amino acids at the equivalent positions within the Dmc1 filament exhibit a broad functional landscape. This work helps highlight the distinct evolutionary trajectories of these two eukaryotic recombinases, which may have contributed to their functional and mechanistic divergence.
History
DepositionAug 12, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46565.png

Downloads & links

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Map

FileDownload / File: emd_46565.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the yeast Dmc1 filament bound to ssDNA in the presence of ATP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.116
Minimum - Maximum-0.17786387 - 0.479795
Average (Standard dev.)0.003526941 (±0.02297252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_46565_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_46565_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of yeast Dmc1 filament bound on ssDNA in the pr...

EntireName: Cryo-EM structure of yeast Dmc1 filament bound on ssDNA in the presence of ATP
Components
  • Complex: Cryo-EM structure of yeast Dmc1 filament bound on ssDNA in the presence of ATP
    • Protein or peptide: Meiotic recombination protein DMC1
    • 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: Cryo-EM structure of yeast Dmc1 filament bound on ssDNA in the pr...

SupramoleculeName: Cryo-EM structure of yeast Dmc1 filament bound on ssDNA in the presence of ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Meiotic recombination protein DMC1

MacromoleculeName: Meiotic recombination protein DMC1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 36.657539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVTGTEIDS DTAKNILSVD ELQNYGINAS DLQKLKSGGI YTVNTVLSTT RRHLCKIKGL SEVKVEKIKE AAGKIIQVGF IPATVQLDI RQRVYSLSTG SKQLDSILGG GIMTMSITEV FGEFRCGKTQ MSHTLCVTTQ LPREMGGGEG KVAYIDTEGT F RPERIKQI ...String:
MSVTGTEIDS DTAKNILSVD ELQNYGINAS DLQKLKSGGI YTVNTVLSTT RRHLCKIKGL SEVKVEKIKE AAGKIIQVGF IPATVQLDI RQRVYSLSTG SKQLDSILGG GIMTMSITEV FGEFRCGKTQ MSHTLCVTTQ LPREMGGGEG KVAYIDTEGT F RPERIKQI AEGYELDPES CLANVSYARA LNSEHQMELV EQLGEELSSG DYRLIVVDSI MANFRVDYCG RGELSERQQK LN QHLFKLN RLAEEFNVAV FLTNQVQSDP GASALFASAD GRKPIGGHVL AHASATRILL RKGRGDERVA KLQDSPDMPE KEC VYVIGE KGITDSSD

UniProtKB: Meiotic recombination protein DMC1

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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 #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / 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
Processinghelical 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: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 16.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 56 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 364408
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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