+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3834 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of an unphosphorylated MCM double hexamer | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.77 Å | |||||||||
Authors | Abid Ali F | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Cryo-EM structure of a licensed DNA replication origin. Authors: Ferdos Abid Ali / Max E Douglas / Julia Locke / Valerie E Pye / Andrea Nans / John F X Diffley / Alessandro Costa / Abstract: Eukaryotic origins of replication are licensed upon loading of the MCM helicase motor onto DNA. ATP hydrolysis by MCM is required for loading and the post-catalytic MCM is an inactive double hexamer ...Eukaryotic origins of replication are licensed upon loading of the MCM helicase motor onto DNA. ATP hydrolysis by MCM is required for loading and the post-catalytic MCM is an inactive double hexamer that encircles duplex DNA. Origin firing depends on MCM engagement of Cdc45 and GINS to form the CMG holo-helicase. CMG assembly requires several steps including MCM phosphorylation by DDK. To understand origin activation, here we have determined the cryo-EM structures of DNA-bound MCM, either unmodified or phosphorylated, and visualize a phospho-dependent MCM element likely important for Cdc45 recruitment. MCM pore loops touch both the Watson and Crick strands, constraining duplex DNA in a bent configuration. By comparing our new MCM-DNA structure with the structure of CMG-DNA, we suggest how the conformational transition from the loaded, post-catalytic MCM to CMG might promote DNA untwisting and melting at the onset of replication. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3834.map.gz | 6.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3834-v30.xml emd-3834.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3834_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_3834.png | 71.8 KB | ||
Others | emd_3834_half_map_1.map.gz emd_3834_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3834 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3834 | HTTPS FTP |
-Validation report
Summary document | emd_3834_validation.pdf.gz | 403.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3834_full_validation.pdf.gz | 402.8 KB | Display | |
Data in XML | emd_3834_validation.xml.gz | 15 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3834 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3834 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3834.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: #1
File | emd_3834_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_3834_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Saccharomyces cerevisiae unphosphorylated MCM double hexamer
Entire | Name: Saccharomyces cerevisiae unphosphorylated MCM double hexamer |
---|---|
Components |
|
-Supramolecule #1: Saccharomyces cerevisiae unphosphorylated MCM double hexamer
Supramolecule | Name: Saccharomyces cerevisiae unphosphorylated MCM double hexamer type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 1.2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.67 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |