+Open data
-Basic information
Entry | Database: PDB / ID: 7ej6 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Yeast Dmc1 presynaptic complex | ||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||
Keywords | DNA BINDING PROTEIN/DNA / Yeast meiotic recombination protein DMC1 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||||||||||||||
Function / homology | ADENOSINE-5'-TRIPHOSPHATE / DNA / : Function and homology information | ||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.21 Å | ||||||||||||||||||||||||
Authors | Zhao, L.Y. / Xu, J.F. / Wang, H.W. | ||||||||||||||||||||||||
Funding support | China, 7items
| ||||||||||||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ej6.cif.gz | 175.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ej6.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ej6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ej6_validation.pdf.gz | 968 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ej6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7ej6_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 7ej6_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/7ej6 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/7ej6 | HTTPS FTP |
-Related structure data
Related structure data | 31153MC 7ej7C 7ejcC 7ejeC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 36657.539 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PACBIOSEQ_LOCUS2179, SCNYR20_0011024600, SCP684_0011023900 Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L0Z498 #2: DNA chain | | Mass: 2692.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Yeast Dmc1 presynaptic complex / Type: COMPLEX Details: 3.21 angstrom cryoEM structure of yeast Dmc1-ssDNA presynaptic complex Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 56.7 ° / Axial rise/subunit: 15.88 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225795 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
|