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Open data
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Basic information
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Title | Yeast Dmc1 presynaptic complex | ||||||||||||||||||||||||
![]() | 3.21 angstrom resolution cryoEM structure of yeast Dmc1-ssDNA presynaptic complex | ||||||||||||||||||||||||
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![]() | Yeast meiotic recombination protein DMC1 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||||||||||||||
Function / homology | : ![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.21 Å | ||||||||||||||||||||||||
![]() | Zhao LY / Xu JF / Wang HW | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 21.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.7 KB 12.7 KB | Display Display | ![]() |
Images | ![]() | 208.8 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ej6MC ![]() 7ej7C ![]() 7ejcC ![]() 7ejeC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | 3.21 angstrom resolution cryoEM structure of yeast Dmc1-ssDNA presynaptic complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.885 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Yeast Dmc1 presynaptic complex
Entire | Name: Yeast Dmc1 presynaptic complex |
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Components |
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-Supramolecule #1: Yeast Dmc1 presynaptic complex
Supramolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: HLJ1_G0016300.mRNA.1.CDS.1
Macromolecule | Name: HLJ1_G0016300.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.657539 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Macromolecule | Name: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.692778 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 reconstruction | Applied 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 |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Final angle assignment | Type: NOT APPLICABLE |