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Yorodumi- EMDB-17204: Cryo-EM structure of CMG helicase bound to TIM-1/TIPN-1 and homod... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17204 | |||||||||
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Title | Cryo-EM structure of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans) | |||||||||
Map data | Cryo-EM density map of the Caenorhabditis elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA | |||||||||
Sample |
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Keywords | DNA Replication / DNA Replication Initiation / Replisome / DONSON / Replication | |||||||||
Function / homology | Function and homology information MCM complex assembly / : / Unwinding of DNA / Assembly of the pre-replicative complex / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / Orc1 removal from chromatin / : / regulation of sister chromatid cohesion / replication fork arrest ...MCM complex assembly / : / Unwinding of DNA / Assembly of the pre-replicative complex / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / Orc1 removal from chromatin / : / regulation of sister chromatid cohesion / replication fork arrest / gonad development / cell cycle phase transition / DNA strand elongation involved in mitotic DNA replication / GINS complex / nuclear DNA replication / mitotic DNA replication preinitiation complex assembly / meiotic sister chromatid cohesion / mitotic DNA replication / DNA replication checkpoint signaling / DNA replication preinitiation complex / MCM complex / locomotion / pronucleus / replication fork protection complex / double-strand break repair via break-induced replication / cell cycle / mitotic DNA replication initiation / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching / regulation of DNA-templated DNA replication initiation / DNA duplex unwinding / mitotic sister chromatid cohesion / DNA strand elongation involved in DNA replication / DNA unwinding involved in DNA replication / replication fork processing / mitotic sister chromatid segregation / DNA replication origin binding / DNA replication initiation / condensed chromosome / DNA helicase activity / meiotic cell cycle / helicase activity / DNA-templated DNA replication / chromosome / nervous system development / single-stranded DNA binding / DNA helicase / DNA replication / hydrolase activity / cell division / DNA repair / chromatin binding / positive regulation of cell population proliferation / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Jenkyn-Bedford M / Yeeles JTP / Labib KPM | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Science / Year: 2023 Title: DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in . Authors: Yisui Xia / Remi Sonneville / Michael Jenkyn-Bedford / Liqin Ji / Constance Alabert / Ye Hong / Joseph T P Yeeles / Karim P M Labib / Abstract: Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that ...Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that are not present in yeast. In this work, we show that DNSN-1, the ortholog of human DONSON, functions during helicase assembly in a complex with MUS-101/TOPBP1. DNSN-1 is required to recruit the GINS complex to chromatin, and a cryo-electron microscopy structure indicates that DNSN-1 positions GINS on the MCM-2-7 helicase motor (comprising the six MCM-2 to MCM-7 proteins), by direct binding of DNSN-1 to GINS and MCM-3, using interfaces that we show are important for initiation and essential for viability. These findings identify DNSN-1 as a missing link in our understanding of DNA replication initiation, suggesting that initiation defects underlie the human disease syndrome that results from DONSON mutations. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17204.map.gz | 5.2 MB | EMDB map data format | |
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Header (meta data) | emd-17204-v30.xml emd-17204.xml | 40.7 KB 40.7 KB | Display Display | EMDB header |
Images | emd_17204.png | 100.6 KB | ||
Filedesc metadata | emd-17204.cif.gz | 12.5 KB | ||
Others | emd_17204_half_map_1.map.gz emd_17204_half_map_2.map.gz | 45 MB 45 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17204 | HTTPS FTP |
-Validation report
Summary document | emd_17204_validation.pdf.gz | 633.6 KB | Display | EMDB validaton report |
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Full document | emd_17204_full_validation.pdf.gz | 633.2 KB | Display | |
Data in XML | emd_17204_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_17204_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17204 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17204 | HTTPS FTP |
-Related structure data
Related structure data | 8ouwMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17204.map.gz / Format: CCP4 / Size: 120.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM density map of the Caenorhabditis elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.295 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map 2. Cryo-EM density map of the Caenorhabditis...
File | emd_17204_half_map_1.map | ||||||||||||
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Annotation | Half-map 2. Cryo-EM density map of the Caenorhabditis elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1. Cryo-EM density map of the Caenorhabditis...
File | emd_17204_half_map_2.map | ||||||||||||
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Annotation | Half-map 1. Cryo-EM density map of the Caenorhabditis elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNS...
+Supramolecule #1: Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNS...
+Macromolecule #1: DNA replication licensing factor MCM2
+Macromolecule #2: DNA replication licensing factor MCM3
+Macromolecule #3: DNA replication licensing factor mcm-4
+Macromolecule #4: DNA replication licensing factor mcm-5
+Macromolecule #5: DNA replication licensing factor mcm-6
+Macromolecule #6: DNA replication licensing factor MCM7
+Macromolecule #7: Probable DNA replication complex GINS protein PSF1
+Macromolecule #8: Probable DNA replication complex GINS protein PSF2
+Macromolecule #9: DNA replication complex GINS protein PSF3
+Macromolecule #10: DNA replication complex GINS protein SLD5
+Macromolecule #11: Cell division control protein 45 homolog
+Macromolecule #12: Downstream Neighbor of SoN homolog
+Macromolecule #14: Protein timeless homolog
+Macromolecule #15: Protein TIPIN homolog
+Macromolecule #13: DNA Leading Strand Template
+Macromolecule #16: DNA Lagging Strand Template
+Macromolecule #17: ZINC ION
+Macromolecule #18: MAGNESIUM ION
+Macromolecule #19: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Details: 15 mA |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.7 sec. / Average electron dose: 40.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33900 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |