+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1822 | |||||||||
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Title | Yeast Anaphase Promoting Complex (Dimer) | |||||||||
Map data | 3D structure of the Yeast Anaphase Promoting Complex (Dimer) | |||||||||
Sample |
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Keywords | Anaphase / Yeast / Cell cycle | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 35.0 Å | |||||||||
Authors | Buschhorn BA / Petzold G / Galova M / Dube P / Kraft C / Herzog F / Peters JM / Stark H | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2011 Title: Substrate binding on the APC/C occurs between the coactivator Cdh1 and the processivity factor Doc1. Authors: Bettina A Buschhorn / Georg Petzold / Marta Galova / Prakash Dube / Claudine Kraft / Franz Herzog / Holger Stark / Jan-Michael Peters / Abstract: The anaphase-promoting complex/cyclosome (APC/C) is a 22S ubiquitin ligase complex that initiates chromosome segregation and mitotic exit. We have used biochemical and electron microscopic analyses ...The anaphase-promoting complex/cyclosome (APC/C) is a 22S ubiquitin ligase complex that initiates chromosome segregation and mitotic exit. We have used biochemical and electron microscopic analyses of Saccharomyces cerevisiae and human APC/C to address how the APC/C subunit Doc1 contributes to recruitment and processive ubiquitylation of APC/C substrates, and to understand how APC/C monomers interact to form a 36S dimeric form. We show that Doc1 interacts with Cdc27, Cdc16 and Apc1 and is located in the vicinity of the cullin-RING module Apc2-Apc11 in the inner cavity of the APC/C. Substrate proteins also bind in the inner cavity, in close proximity to Doc1 and the coactivator Cdh1, and induce conformational changes in Apc2-Apc11. Our results suggest that substrates are recruited to the APC/C by binding to a bipartite substrate receptor composed of a coactivator protein and Doc1. | |||||||||
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_1822.map.gz | 941.9 KB | EMDB map data format | |
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Header (meta data) | emd-1822-v30.xml emd-1822.xml | 6.8 KB 6.8 KB | Display Display | EMDB header |
Images | emd_1822.png | 145.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1822 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1822 | HTTPS FTP |
-Validation report
Summary document | emd_1822_validation.pdf.gz | 240.1 KB | Display | EMDB validaton report |
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Full document | emd_1822_full_validation.pdf.gz | 239.2 KB | Display | |
Data in XML | emd_1822_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1822 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1822 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1822.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D structure of the Yeast Anaphase Promoting Complex (Dimer) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.2 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 : Yeast anaphase promoting complex (Dimer)
Entire | Name: Yeast anaphase promoting complex (Dimer) |
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Components |
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-Supramolecule #1000: Yeast anaphase promoting complex (Dimer)
Supramolecule | Name: Yeast anaphase promoting complex (Dimer) / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: APCC
Supramolecule | Name: APCC / type: organelle_or_cellular_component / ID: 1 / Name.synonym: APCC / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' yeast |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE / Details: Staining with 1% uranyl formate |
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Vitrification | Cryogen name: NITROGEN / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Image recording | Digitization - Sampling interval: 1.8 µm |
Electron beam | Acceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1271 |
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