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- EMDB-31153: Yeast Dmc1 presynaptic complex -

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Basic information

Entry
Database: EMDB / ID: EMD-31153
TitleYeast Dmc1 presynaptic complex
Map data3.21 angstrom resolution cryoEM structure of yeast Dmc1-ssDNA presynaptic complex
Sample
  • Complex: Yeast Dmc1 presynaptic complex
    • Protein or peptide: HLJ1_G0016300.mRNA.1.CDS.1
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsYeast meiotic recombination protein DMC1 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology:
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsZhao LY / Xu JF / Wang HW
Funding support China, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700654 China
National Natural Science Foundation of China (NSFC)31825009 China
National Natural Science Foundation of China (NSFC)21877069 China
National Natural Science Foundation of China (NSFC)21922704 China
National Natural Science Foundation of China (NSFC)31570754 China
National Natural Science Foundation of China (NSFC)21625302 China
National Natural Science Foundation of China (NSFC)21933010 China
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination.
Authors: Jingfei Xu / Lingyun Zhao / Sijia Peng / Huiying Chu / Rui Liang / Meng Tian / Philip P Connell / Guohui Li / Chunlai Chen / Hong-Wei Wang /
Abstract: Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for ...Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for DNA repair in somatic cells during mitosis while Dmc1 only works during meiosis in germ cells. This spatiotemporal difference is probably due to their distinctive mismatch tolerance during HR: Rad51 does not permit HR in the presence of mismatches, whereas Dmc1 can tolerate certain mismatches. Here, the cryo-EM structures of Rad51-DNA and Dmc1-DNA complexes revealed that the major conformational differences between these two proteins are located in their Loop2 regions, which contain invading single-stranded DNA (ssDNA) binding residues and double-stranded DNA (dsDNA) complementary strand binding residues, stabilizing ssDNA and dsDNA in presynaptic and postsynaptic complexes, respectively. By combining molecular dynamic simulation and single-molecule FRET assays, we identified that V273 and D274 in the Loop2 region of human RAD51 (hRAD51), corresponding to P274 and G275 of human DMC1 (hDMC1), are the key residues regulating mismatch tolerance during strand exchange in HR. This HR accuracy control mechanism provides mechanistic insights into the specific roles of Rad51 and Dmc1 in DNA double-strand break repair and may shed light on the regulatory mechanism of genetic recombination in mitosis and meiosis.
History
DepositionApr 1, 2021-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31153.png

Downloads & links

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Map

FileDownload / File: emd_31153.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.21 angstrom resolution cryoEM structure of yeast Dmc1-ssDNA presynaptic complex
Voxel sizeX=Y=Z: 0.885 Å
Density
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.09183139 - 0.28422228
Average (Standard dev.)0.0008489205 (±0.00961221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 354.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yeast Dmc1 presynaptic complex

EntireName: Yeast Dmc1 presynaptic complex
Components
  • Complex: Yeast Dmc1 presynaptic complex
    • Protein or peptide: HLJ1_G0016300.mRNA.1.CDS.1
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Yeast Dmc1 presynaptic complex

SupramoleculeName: Yeast Dmc1 presynaptic complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: 3.21 angstrom cryoEM structure of yeast Dmc1-ssDNA presynaptic complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: HLJ1_G0016300.mRNA.1.CDS.1

MacromoleculeName: HLJ1_G0016300.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / 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: UNIPROTKB: A0A6L0Z498

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Macromolecule #2: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(P*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: 2.692778 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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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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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 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: 15.88 Å
Applied symmetry - Helical parameters - Δ&Phi: 56.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225795
Startup modelType of model: EMDB MAP
EMDB ID:

9566

Final angle assignmentType: NOT APPLICABLE

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