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- EMDB-49488: The Cryo-EM structure of the yeast Dmc1-ssDNA nucleoprotein filam... -

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Basic information

Entry
Database: EMDB / ID: EMD-49488
TitleThe Cryo-EM structure of the yeast Dmc1-ssDNA nucleoprotein filament ADP bound state
Map datatructure of the yeast Dmc1-ssDNA nucleoprotein filament ADP bound state
Sample
  • Complex: Cryo-EM structure of yeast Dmc1 - ssDNA nucleoprotein filament ADP bound state
    • Protein or peptide: Meiotic recombination protein DMC1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsDNA Repair / Homologous Recombination / DNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 Dmc1-ssDNA nucleoprotein filament ADP bound state
Authors: Shin Y / Greene EC
History
DepositionFeb 27, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49488.png

Downloads & links

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Map

FileDownload / File: emd_49488.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtructure of the yeast Dmc1-ssDNA nucleoprotein filament ADP bound state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.28 Å		0.82 Å/pix.
x 360 pix.
= 296.28 Å		0.82 Å/pix.
x 360 pix.
= 296.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.823 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4639826 - 0.6696886
Average (Standard dev.)0.0004454694 (±0.015041915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49488_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49488_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_49488_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 - ssDNA nucleoprotein filament AD...

EntireName: Cryo-EM structure of yeast Dmc1 - ssDNA nucleoprotein filament ADP bound state
Components
  • Complex: Cryo-EM structure of yeast Dmc1 - ssDNA nucleoprotein filament ADP bound state
    • Protein or peptide: Meiotic recombination protein DMC1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of yeast Dmc1 - ssDNA nucleoprotein filament AD...

SupramoleculeName: Cryo-EM structure of yeast Dmc1 - 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: 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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 3 / 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: 3 / 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: 58.0 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 960233
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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