[English] 日本語
Yorodumi- EMDB-23755: CryoEM map of the structure of the S. cerevisiae origin recogniti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23755 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM map of the structure of the S. cerevisiae origin recognition complex bound to the replication initiator Cdc6 and the ARS1 origin DNA. | |||||||||||||||
Map data | ||||||||||||||||
Sample |
| |||||||||||||||
Keywords | replication initiation / REPLICATION | |||||||||||||||
Function / homology | Function and homology information MCM complex loading / CDC6 association with the ORC:origin complex / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / Assembly of the ORC complex at the origin of replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / nucleosome organization / nuclear pre-replicative complex ...MCM complex loading / CDC6 association with the ORC:origin complex / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / Assembly of the ORC complex at the origin of replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / nucleosome organization / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / mitotic DNA replication checkpoint signaling / regulation of DNA-templated DNA replication initiation / silent mating-type cassette heterochromatin formation / CDK-mediated phosphorylation and removal of Cdc6 / Orc1 removal from chromatin / regulation of DNA replication / DNA replication origin binding / nucleosome binding / subtelomeric heterochromatin formation / DNA replication initiation / G1/S transition of mitotic cell cycle / chromosome / chromosome, telomeric region / cell division / GTPase activity / chromatin binding / GTP binding / 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: 3.6 Å | |||||||||||||||
Authors | Feng X / Li H | |||||||||||||||
Funding support | United States, 4 items
| |||||||||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Authors: Xiang Feng / Yasunori Noguchi / Marta Barbon / Bruce Stillman / Christian Speck / Huilin Li / Abstract: The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell ...The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. It has been unclear at the molecular level how Cdc6 activates ORC, converting it to an active recruiter of the Mcm2-7 hexamer, the core of the replicative helicase. Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC-Cdc6 bound to an 85-bp ARS1 origin DNA. The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. The results illuminate the molecular mechanism of a critical biochemical step in the licensing of eukaryotic replication origins. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23755.map.gz | 12.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23755-v30.xml emd-23755.xml | 30.9 KB 30.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23755_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_23755.png | 95.9 KB | ||
Filedesc metadata | emd-23755.cif.gz | 9.5 KB | ||
Others | emd_23755_half_map_1.map.gz emd_23755_half_map_2.map.gz | 65.4 MB 65.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23755 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23755 | HTTPS FTP |
-Validation report
Summary document | emd_23755_validation.pdf.gz | 916.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23755_full_validation.pdf.gz | 916.3 KB | Display | |
Data in XML | emd_23755_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | emd_23755_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23755 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23755 | HTTPS FTP |
-Related structure data
Related structure data | 7mcaMC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_23755.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: #2
File | emd_23755_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_23755_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Complex of origin replication complex with Cdc6 and ARS1 origin DNA
+Supramolecule #1: Complex of origin replication complex with Cdc6 and ARS1 origin DNA
+Macromolecule #1: Origin recognition complex subunit 1
+Macromolecule #2: Origin recognition complex subunit 2
+Macromolecule #3: Origin recognition complex subunit 3
+Macromolecule #4: Origin recognition complex subunit 4
+Macromolecule #5: Origin recognition complex subunit 5
+Macromolecule #6: Origin recognition complex subunit 6
+Macromolecule #9: Cell division control protein 6
+Macromolecule #7: DNA (85-MER)
+Macromolecule #8: DNA (85-MER)
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 76.0 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 |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
---|---|
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 118.5 / Target criteria: correlation coefficient |
Output model | PDB-7mca: |