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Yorodumi- EMDB-25926: S. cerevisiae ORC bound to 84 bp ARS1 DNA and Cdc6 (state 2) with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25926 | ||||||||||||
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Title | S. cerevisiae ORC bound to 84 bp ARS1 DNA and Cdc6 (state 2) with flexible Orc6 N-terminal domain | ||||||||||||
Map data | unsharpened cryo-EM map | ||||||||||||
Sample |
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Keywords | initiator / helicase loader / AAA+ ATPase / REPLICATION-DNA complex | ||||||||||||
Function / homology | Function and homology information 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 / CDK-mediated phosphorylation and removal of Cdc6 / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Orc1 removal from chromatin / Activation of the pre-replicative complex / nuclear pre-replicative complex ...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 / CDK-mediated phosphorylation and removal of Cdc6 / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Orc1 removal from chromatin / Activation of the pre-replicative complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / regulation of DNA replication / DNA replication origin binding / subtelomeric heterochromatin formation / DNA replication initiation / nucleosome binding / 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: 2.7 Å | ||||||||||||
Authors | Schmidt JM / Yang R | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6. Authors: Jan Marten Schmidt / Ran Yang / Ashish Kumar / Olivia Hunker / Jan Seebacher / Franziska Bleichert / Abstract: The coordinated action of multiple replicative helicase loading factors is needed for the licensing of replication origins prior to DNA replication. Binding of the Origin Recognition Complex (ORC) to ...The coordinated action of multiple replicative helicase loading factors is needed for the licensing of replication origins prior to DNA replication. Binding of the Origin Recognition Complex (ORC) to DNA initiates the ATP-dependent recruitment of Cdc6, Cdt1 and Mcm2-7 loading, but the structural details for timely ATPase site regulation and for how loading can be impeded by inhibitory signals, such as cyclin-dependent kinase phosphorylation, are unknown. Using cryo-electron microscopy, we have determined several structures of S. cerevisiae ORC·DNA·Cdc6 intermediates at 2.5-2.7 Å resolution. These structures reveal distinct ring conformations of the initiator·co-loader assembly and inactive ATPase site configurations for ORC and Cdc6. The Orc6 N-terminal domain laterally engages the ORC·Cdc6 ring in a manner that is incompatible with productive Mcm2-7 docking, while deletion of this Orc6 region alleviates the CDK-mediated inhibition of Mcm7 recruitment. Our findings support a model in which Orc6 promotes the assembly of an autoinhibited ORC·DNA·Cdc6 intermediate to block origin licensing in response to CDK phosphorylation and to avert DNA re-replication. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25926.map.gz | 80.7 MB | EMDB map data format | |
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Header (meta data) | emd-25926-v30.xml emd-25926.xml | 32.5 KB 32.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25926_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_25926.png | 115 KB | ||
Filedesc metadata | emd-25926.cif.gz | 9.1 KB | ||
Others | emd_25926_additional_1.map.gz emd_25926_additional_2.map.gz emd_25926_half_map_1.map.gz emd_25926_half_map_2.map.gz | 10 MB 14.3 MB 80.9 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25926 | HTTPS FTP |
-Related structure data
Related structure data | 7tjiMC 7tjfC 7tjhC 7tjjC 7tjkC C: citing same article (ref.) M: atomic model generated by this map |
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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_25926.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened cryo-EM map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: sharpened, masked cryo-EM map
File | emd_25926_additional_1.map | ||||||||||||
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Annotation | sharpened, masked cryo-EM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: density modified cryo-EM map
File | emd_25926_additional_2.map | ||||||||||||
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Annotation | density modified cryo-EM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_25926_half_map_1.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_25926_half_map_2.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : ORC in complex with ARS1 DNA and Cdc6
+Supramolecule #1: ORC in complex with ARS1 DNA and Cdc6
+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, 84 bp ARS1
+Macromolecule #8: DNA, 84 bp ARS1
+Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 6.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |