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Yorodumi- EMDB-1841: Structural basis for the subunit assembly of the anaphase promoti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1841 | |||||||||
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Title | Structural basis for the subunit assembly of the anaphase promoting complex | |||||||||
Map data | Anaphase promoting complex TPR6 subcomplex | |||||||||
Sample |
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Keywords | anaphase promoting complex / cyclosome / APC / APC/C / cell cycle / D-box / KEN-box / co-activator / Cdh1 / tetraticopeptide repeats / TPR / ubiquitylation / cyclin | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining | |||||||||
Authors | Schreiber A / Stengel F / Zhang Z / Enchev RE / Kong E / Morris EP / Robinson CV / daFonseca PCA / Barford D | |||||||||
Citation | Journal: Nature / Year: 2011 Title: Structural basis for the subunit assembly of the anaphase-promoting complex. Authors: Anne Schreiber / Florian Stengel / Ziguo Zhang / Radoslav I Enchev / Eric H Kong / Edward P Morris / Carol V Robinson / Paula C A da Fonseca / David Barford / Abstract: The anaphase-promoting complex or cyclosome (APC/C) is an unusually large E3 ubiquitin ligase responsible for regulating defined cell cycle transitions. Information on how its 13 constituent proteins ...The anaphase-promoting complex or cyclosome (APC/C) is an unusually large E3 ubiquitin ligase responsible for regulating defined cell cycle transitions. Information on how its 13 constituent proteins are assembled, and how they interact with co-activators, substrates and regulatory proteins is limited. Here, we describe a recombinant expression system that allows the reconstitution of holo APC/C and its sub-complexes that, when combined with electron microscopy, mass spectrometry and docking of crystallographic and homology-derived coordinates, provides a precise definition of the organization and structure of all essential APC/C subunits, resulting in a pseudo-atomic model for 70% of the APC/C. A lattice-like appearance of the APC/C is generated by multiple repeat motifs of most APC/C subunits. Three conserved tetratricopeptide repeat (TPR) subunits (Cdc16, Cdc23 and Cdc27) share related superhelical homo-dimeric architectures that assemble to generate a quasi-symmetrical structure. Our structure explains how this TPR sub-complex, together with additional scaffolding subunits (Apc1, Apc4 and Apc5), coordinate the juxtaposition of the catalytic and substrate recognition module (Apc2, Apc11 and Apc10 (also known as Doc1)), and TPR-phosphorylation sites, relative to co-activator, regulatory proteins and substrates. | |||||||||
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_1841.map.gz | 10 MB | EMDB map data format | |
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Header (meta data) | emd-1841-v30.xml emd-1841.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
Images | figure_EBI1841.tif | 130.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1841 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1841 | HTTPS FTP |
-Validation report
Summary document | emd_1841_validation.pdf.gz | 184.3 KB | Display | EMDB validaton report |
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Full document | emd_1841_full_validation.pdf.gz | 183.4 KB | Display | |
Data in XML | emd_1841_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1841 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1841 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1841.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Anaphase promoting complex TPR6 subcomplex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.47 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 : Anaphase promoting complex TPR6 subcomplex
Entire | Name: Anaphase promoting complex TPR6 subcomplex |
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Components |
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-Supramolecule #1000: Anaphase promoting complex TPR6 subcomplex
Supramolecule | Name: Anaphase promoting complex TPR6 subcomplex / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: Anaphase promoting complex TPR6 subcomplex
Macromolecule | Name: Anaphase promoting complex TPR6 subcomplex / type: protein_or_peptide / ID: 1 / Name.synonym: Anaphase promoting complex TPR6 subcomplex / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' Yeast |
Recombinant expression | Organism: Baculovirus/Insect Cells |
-Macromolecule #2: Cdh1
Macromolecule | Name: Cdh1 / type: protein_or_peptide / ID: 2 / Name.synonym: Cdh1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' yeast |
Recombinant expression | Organism: Baculovirus/Insect cells |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE / Details: Grids were stained using 2% w/v uranyl acetate |
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Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Details | Sample stained using uranyl acetate and imaged at room temperature |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 100 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000 |
Sample stage | Specimen holder: Room temperature side entry / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) |
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