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Yorodumi- EMDB-4467: Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2delD1-Cks2 comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4467 | |||||||||
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Title | Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2delD1-Cks2 complex (with the D1 box mutated) | |||||||||
Map data | unsharpened map | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Zhang S / Barford D | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Cyclin A2 degradation during the spindle assembly checkpoint requires multiple binding modes to the APC/C. Authors: Suyang Zhang / Thomas Tischer / David Barford / Abstract: The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are ...The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are both targeted for degradation by the APC/C, during the spindle assembly checkpoint (SAC), the mitotic checkpoint complex (MCC) represses APC/C's activity towards cyclin B1, but not cyclin A2. Through structural, biochemical and in vivo analysis, we identify a non-canonical D box (D2) that is critical for cyclin A2 ubiquitination in vitro and degradation in vivo. During the SAC, cyclin A2 is ubiquitinated by the repressed APC/C-MCC, mediated by the cooperative engagement of its KEN and D2 boxes, ABBA motif, and the cofactor Cks. Once the SAC is satisfied, cyclin A2 binds APC/C-Cdc20 through two mutually exclusive binding modes, resulting in differential ubiquitination efficiency. Our findings reveal that a single substrate can engage an E3 ligase through multiple binding modes, affecting its degradation timing and efficiency. | |||||||||
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_4467.map.gz | 194.2 MB | EMDB map data format | |
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Header (meta data) | emd-4467-v30.xml emd-4467.xml | 37.6 KB 37.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4467_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_4467.png | 56.1 KB | ||
Others | emd_4467_additional.map.gz emd_4467_additional_1.map.gz emd_4467_half_map_1.map.gz emd_4467_half_map_2.map.gz | 16.9 MB 16.9 MB 194.5 MB 194.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4467 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4467 | HTTPS FTP |
-Validation report
Summary document | emd_4467_validation.pdf.gz | 455 KB | Display | EMDB validaton report |
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Full document | emd_4467_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | emd_4467_validation.xml.gz | 19.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4467 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4467 | HTTPS FTP |
-Related structure data
Related structure data | 4463C 4464C 4465C 4466C 6q6gC 6q6hC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4467.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: sharpened map with a B factor -50
File | emd_4467_additional.map | ||||||||||||
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Annotation | sharpened map with a B factor -50 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: sharpened map with a B factor -50
File | emd_4467_additional_1.map | ||||||||||||
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Annotation | sharpened map with a B factor -50 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap1
File | emd_4467_half_map_1.map | ||||||||||||
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Annotation | halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap2
File | emd_4467_half_map_2.map | ||||||||||||
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Annotation | halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : APC/C-Cdc20-Cdk2-cyclinA2delD1-Cks2 complex (with the D1 box mutated)
+Supramolecule #1: APC/C-Cdc20-Cdk2-cyclinA2delD1-Cks2 complex (with the D1 box mutated)
+Macromolecule #1: Apc1
+Macromolecule #2: Apc2
+Macromolecule #3: Apc3
+Macromolecule #4: Apc4
+Macromolecule #5: Apc5
+Macromolecule #6: Apc6
+Macromolecule #7: Apc7
+Macromolecule #8: Apc8
+Macromolecule #9: Apc10
+Macromolecule #10: Apc11
+Macromolecule #11: Apc12
+Macromolecule #12: Apc13
+Macromolecule #13: Apc15
+Macromolecule #14: Apc16
+Macromolecule #15: Cdc20
+Macromolecule #16: Cdk2
+Macromolecule #17: Cyclin A2
+Macromolecule #18: Cks2
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 8 / Details: 20mM Hepes, 150mM NaCl, 0.5mM TCEP |
Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |