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Yorodumi- EMDB-1815: The structure of anaphase promoting complex-Cdh1-Dbox at 10 Angst... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1815 | |||||||||
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Title | The structure of anaphase promoting complex-Cdh1-Dbox at 10 Angstroms resolution | |||||||||
Map data | The anaphase promoting complex-Cdh1-Dbox at 10 Angstroms resolution | |||||||||
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 / cryo EM / Resolution: 11.0 Å | |||||||||
Authors | daFonseca PCA / Kong EH / Zhang Z / Schreiber A / Williams MA / Morris EP / Barford D | |||||||||
Citation | Journal: Nature / Year: 2011 Title: Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor. Authors: Paula C A da Fonseca / Eric H Kong / Ziguo Zhang / Anne Schreiber / Mark A Williams / Edward P Morris / David Barford / Abstract: The ubiquitylation of cell-cycle regulatory proteins by the large multimeric anaphase-promoting complex (APC/C) controls sister chromatid segregation and the exit from mitosis. Selection of APC/C ...The ubiquitylation of cell-cycle regulatory proteins by the large multimeric anaphase-promoting complex (APC/C) controls sister chromatid segregation and the exit from mitosis. Selection of APC/C targets is achieved through recognition of destruction motifs, predominantly the destruction (D)-box and KEN (Lys-Glu-Asn)-box. Although this process is known to involve a co-activator protein (either Cdc20 or Cdh1) together with core APC/C subunits, the structural basis for substrate recognition and ubiquitylation is not understood. Here we investigate budding yeast APC/C using single-particle electron microscopy and determine a cryo-electron microscopy map of APC/C in complex with the Cdh1 co-activator protein (APC/C(Cdh1)) bound to a D-box peptide at ∼10 Å resolution. We find that a combined catalytic and substrate-recognition module is located within the central cavity of the APC/C assembled from Cdh1, Apc10--a core APC/C subunit previously implicated in substrate recognition--and the cullin domain of Apc2. Cdh1 and Apc10, identified from difference maps, create a co-receptor for the D-box following repositioning of Cdh1 towards Apc10. Using NMR spectroscopy we demonstrate specific D-box-Apc10 interactions, consistent with a role for Apc10 in directly contributing towards D-box recognition by the APC/C(Cdh1) complex. Our results rationalize the contribution of both co-activator and core APC/C subunits to D-box recognition and provide a structural framework for understanding mechanisms of substrate recognition and catalysis by the APC/C. | |||||||||
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_1815.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-1815-v30.xml emd-1815.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | figure_EMD1815.tif | 233.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1815 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1815 | HTTPS FTP |
-Validation report
Summary document | emd_1815_validation.pdf.gz | 199.2 KB | Display | EMDB validaton report |
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Full document | emd_1815_full_validation.pdf.gz | 198.3 KB | Display | |
Data in XML | emd_1815_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1815 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1815 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1815.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The anaphase promoting complex-Cdh1-Dbox at 10 Angstroms resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.824 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 : S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-bo...
Entire | Name: S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-box peptide |
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Components |
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-Supramolecule #1000: S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-bo...
Supramolecule | Name: S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-box peptide type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 1.13 MDa |
-Macromolecule #1: Anaphase promoting complex
Macromolecule | Name: Anaphase promoting complex / type: protein_or_peptide / ID: 1 / Name.synonym: Anaphase promoting complex or cyclosome / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 5 seconds before plunging |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 95 K |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF |
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