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Yorodumi- EMDB-1845: Structural basis for the subunit assembly of the anaphase promoti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1845 | |||||||||
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Title | Structural basis for the subunit assembly of the anaphase promoting complex | |||||||||
Map data | SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23) | |||||||||
Sample |
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Keywords | APC/C / anaphase promoting complex | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction | |||||||||
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_1845.map.gz | 9.1 MB | EMDB map data format | |
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Header (meta data) | emd-1845-v30.xml emd-1845.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_1845.tif | 123.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1845 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1845 | HTTPS FTP |
-Validation report
Summary document | emd_1845_validation.pdf.gz | 187 KB | Display | EMDB validaton report |
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Full document | emd_1845_full_validation.pdf.gz | 186.1 KB | Display | |
Data in XML | emd_1845_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1845 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1845 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1845.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)
Entire | Name: SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23) |
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Components |
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-Supramolecule #1000: SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)
Supramolecule | Name: SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23) type: sample / ID: 1000 / Number unique components: 8 |
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Molecular weight | Experimental: 700 KDa / Theoretical: 690 KDa |
-Macromolecule #1: Apc1
Macromolecule | Name: Apc1 / type: protein_or_peptide / ID: 1 / Name.synonym: Apc1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Macromolecule #2: Apc2
Macromolecule | Name: Apc2 / type: protein_or_peptide / ID: 2 / Name.synonym: Apc2 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Macromolecule #3: Apc4
Macromolecule | Name: Apc4 / type: protein_or_peptide / ID: 3 / Name.synonym: Apc4 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Macromolecule #4: Apc5
Macromolecule | Name: Apc5 / type: protein_or_peptide / ID: 4 / Name.synonym: Apc5 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Macromolecule #5: Apc10
Macromolecule | Name: Apc10 / type: protein_or_peptide / ID: 5 / Name.synonym: Apc10 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Macromolecule #6: Apc11
Macromolecule | Name: Apc11 / type: protein_or_peptide / ID: 6 / Name.synonym: Apc11 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Macromolecule #7: Mnd2
Macromolecule | Name: Mnd2 / type: protein_or_peptide / ID: 7 / Name.synonym: Mnd2 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Macromolecule #8: Cdc23
Macromolecule | Name: Cdc23 / type: protein_or_peptide / ID: 8 / Name.synonym: Cdc23 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / 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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