[English] 日本語
Yorodumi- EMDB-4164: Cryo-EM structure of the DNA bound DDK phosphorylated MCM double ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4164 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the DNA bound DDK phosphorylated MCM double hexamer | |||||||||
Map data | None | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / nuclear DNA replication / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / mitotic DNA replication / Activation of the pre-replicative complex / CMG complex ...MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / nuclear DNA replication / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / mitotic DNA replication / Activation of the pre-replicative complex / CMG complex / nuclear pre-replicative complex / MCM complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / replication fork protection complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA unwinding involved in DNA replication / nuclear replication fork / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / DNA helicase activity / helicase activity / transcription elongation by RNA polymerase II / heterochromatin formation / single-stranded DNA binding / chromosome, telomeric region / DNA helicase / chromatin binding / DNA damage response / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Abid Ali F / Douglas ME / Locke J / Pye VE / Nans A / Diffley JFX / Costa A | |||||||||
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_4164.map.gz | 36.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4164-v30.xml emd-4164.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4164_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_4164.png | 97.1 KB | ||
Others | emd_4164_half_map_1.map.gz emd_4164_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4164 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4164 | HTTPS FTP |
-Validation report
Summary document | emd_4164_validation.pdf.gz | 546.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4164_full_validation.pdf.gz | 545.6 KB | Display | |
Data in XML | emd_4164_validation.xml.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4164 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4164 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4164.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: S. cerevisiae DNA bound DDK phosphorylated MCM double...
File | emd_4164_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: S. cerevisiae DNA bound DDK phosphorylated MCM double...
File | emd_4164_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer
Entire | Name: S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer |
---|---|
Components |
|
-Supramolecule #1: S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer
Supramolecule | Name: S. cerevisiae DNA bound DDK phosphorylated 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) / Average electron dose: 1.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |