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Yorodumi- EMDB-3680: Full-length complex of S.cerevisiae Cdt1-MCM in ATPgS-bound state. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3680 | |||||||||
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Title | Full-length complex of S.cerevisiae Cdt1-MCM in ATPgS-bound state. | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.4 Å | |||||||||
Authors | He J / Frigola J / Kinkelin K / Pye VE / Renault L / Douglas M / Remus D / Cherepanov P / Costa A / Diffley JFX | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Cdt1 stabilizes an open MCM ring for helicase loading. Authors: Jordi Frigola / Jun He / Kerstin Kinkelin / Valerie E Pye / Ludovic Renault / Max E Douglas / Dirk Remus / Peter Cherepanov / Alessandro Costa / John F X Diffley / Abstract: ORC, Cdc6 and Cdt1 act together to load hexameric MCM, the motor of the eukaryotic replicative helicase, into double hexamers at replication origins. Here we show that Cdt1 interacts with MCM ...ORC, Cdc6 and Cdt1 act together to load hexameric MCM, the motor of the eukaryotic replicative helicase, into double hexamers at replication origins. Here we show that Cdt1 interacts with MCM subunits Mcm2, 4 and 6, which both destabilizes the Mcm2-5 interface and inhibits MCM ATPase activity. Using X-ray crystallography, we show that Cdt1 contains two winged-helix domains in the C-terminal half of the protein and a catalytically inactive dioxygenase-related N-terminal domain, which is important for MCM loading, but not for subsequent replication. We used these structures together with single-particle electron microscopy to generate three-dimensional models of MCM complexes. These show that Cdt1 stabilizes MCM in a left-handed spiral open at the Mcm2-5 gate. We propose that Cdt1 acts as a brace, holding MCM open for DNA entry and bound to ATP until ORC-Cdc6 triggers ATP hydrolysis by MCM, promoting both Cdt1 ejection and MCM ring closure. | |||||||||
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_3680.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-3680-v30.xml emd-3680.xml | 7.6 KB 7.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3680_fsc.xml | 4.3 KB | Display | FSC data file |
Images | emd_3680.png | 441.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3680 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3680 | HTTPS FTP |
-Validation report
Summary document | emd_3680_validation.pdf.gz | 235.4 KB | Display | EMDB validaton report |
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Full document | emd_3680_full_validation.pdf.gz | 234.5 KB | Display | |
Data in XML | emd_3680_validation.xml.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3680 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3680 | HTTPS FTP |
-Related structure data
Related structure data | 3679C 3681C 5me9C 5meaC 5mebC 5mecC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3680.map.gz / Format: CCP4 / Size: 8 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: 2.7 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 : Full-length yeast Cdt1-MCM complex in ATPgS-bound state.
Entire | Name: Full-length yeast Cdt1-MCM complex in ATPgS-bound state. |
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Components |
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-Supramolecule #1: Full-length yeast Cdt1-MCM complex in ATPgS-bound state.
Supramolecule | Name: Full-length yeast Cdt1-MCM complex in ATPgS-bound state. type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Staining | Type: NEGATIVE / Material: Uranyl formate |
-Electron microscopy
Microscope | JEOL 2100 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |