+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30308 | ||||||||||||
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Title | Human DMC1 post-synaptic complexes | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | meiotic homologous recombination / DNA repair / ATPase / RECOMBINATION / RECOMBINATION-DNA complex | ||||||||||||
Function / homology | Function and homology information female gamete generation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / homologous chromosome pairing at meiosis / DNA strand invasion / double-strand break repair involved in meiotic recombination / mitotic recombination / DNA strand exchange activity / lateral element / reciprocal meiotic recombination ...female gamete generation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / homologous chromosome pairing at meiosis / DNA strand invasion / double-strand break repair involved in meiotic recombination / mitotic recombination / DNA strand exchange activity / lateral element / reciprocal meiotic recombination / oocyte maturation / ATP-dependent DNA damage sensor activity / male meiosis I / spermatid development / ATP-dependent activity, acting on DNA / ovarian follicle development / condensed nuclear chromosome / meiotic cell cycle / Meiotic recombination / single-stranded DNA binding / site of double-strand break / chromosome / double-stranded DNA binding / spermatogenesis / chromosome, telomeric region / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.47 Å | ||||||||||||
Authors | Luo SC / Yeh HY / Chi P / Ho MC / Tsai MD | ||||||||||||
Funding support | Taiwan, 3 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures. Authors: Shih-Chi Luo / Hsin-Yi Yeh / Wei-Hsuan Lan / Yi-Min Wu / Cheng-Han Yang / Hao-Yen Chang / Guan-Chin Su / Chia-Yi Lee / Wen-Jin Wu / Hung-Wen Li / Meng-Chiao Ho / Peter Chi / Ming-Daw Tsai / Abstract: Both high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and ...Both high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open "triplet gate" for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30308.map.gz | 201.8 MB | EMDB map data format | |
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Header (meta data) | emd-30308-v30.xml emd-30308.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30308_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_30308.png | 95.7 KB | ||
Filedesc metadata | emd-30308.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30308 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30308 | HTTPS FTP |
-Validation report
Summary document | emd_30308_validation.pdf.gz | 638.2 KB | Display | EMDB validaton report |
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Full document | emd_30308_full_validation.pdf.gz | 637.8 KB | Display | |
Data in XML | emd_30308_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_30308_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30308 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30308 | HTTPS FTP |
-Related structure data
Related structure data | 7c98MC 7c99C 7c9aC 7c9cC 7cgyC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30308.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : DMC1-dsDNA filament
Entire | Name: DMC1-dsDNA filament |
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Components |
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-Supramolecule #1: DMC1-dsDNA filament
Supramolecule | Name: DMC1-dsDNA filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: DMC1
Supramolecule | Name: DMC1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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-Macromolecule #1: Meiotic recombination protein DMC1/LIM15 homolog
Macromolecule | Name: Meiotic recombination protein DMC1/LIM15 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.731031 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKEDQVVAEE PGFQDEEESL FQDIDLLQKH GINVADIKKL KSVGICTIKG IQMTTRRALC NVKGLSEAKV DKIKEAANKL IEPGFLTAF EYSEKRKMVF HITTGSQEFD KLLGGGIESM AITEAFGEFR TGKTQLSHTL CVTAQLPGAG GYPGGKIIFI D TENTFRPD ...String: MKEDQVVAEE PGFQDEEESL FQDIDLLQKH GINVADIKKL KSVGICTIKG IQMTTRRALC NVKGLSEAKV DKIKEAANKL IEPGFLTAF EYSEKRKMVF HITTGSQEFD KLLGGGIESM AITEAFGEFR TGKTQLSHTL CVTAQLPGAG GYPGGKIIFI D TENTFRPD RLRDIADRFN VDHDAVLDNV LYARAYTSEH QMELLDYVAA KFHEEAGIFK LLIIDSIMAL FRVDFSGRGE LA ERQQKLA QMLSRLQKIS EEYNVAVFVT NQMTADPGAT MTFQADPKKP IGGHILAHAS TTRISLRKGR GELRIAKIYD SPE MPENEA TFAITAGGIG DAKE UniProtKB: Meiotic recombination protein DMC1/LIM15 homolog |
-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: synthetic construct (others) |
Molecular weight | Theoretical: 2.692778 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) |
-Macromolecule #3: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Macromolecule | Name: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 2.773904 KDa |
Sequence | String: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 3 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 Details: 25 mM Tris-HCl, pH 7.5, 50 mM KCl and 1 mM dithiothreitol) containing 2 mM AMP-PNP and 5 mM CaCl2 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: The grids were blotted for 1 sec at 22 degree C with 100% relative humidity and plunge-frozen in liquid ethane cooled by liquid nitrogen using a Vitrobot Mark IV (Thermo Fisher).. |
Details | protein sample were applied onto a pre-glow-discharged graphene-oxide coated Quantifoil holey carbon grid (1.2/1.3, 200 mesh) using published protocol |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Coma free - Residual tilt: 10.0 mrad |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Average exposure time: 5.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |