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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 / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / synaptonemal complex assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / ATPase inhibitor activity / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity ...meiotic joint molecule formation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / synaptonemal complex assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / ATPase inhibitor activity / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / sporulation resulting in formation of a cellular spore / ATP-dependent activity, acting on DNA / condensed nuclear chromosome / meiotic cell cycle / single-stranded DNA binding / double-stranded DNA binding / ATP hydrolysis activity / 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: To Be Published
Title: The cryo-EM structure of the yeast RAD51 filament bound to ssDNA in the presence of ATP
Authors: Shin Y / Greene EC
History
DepositionAug 12, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing 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

Projections

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

Projections

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 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
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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