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- EMDB-4463: Cryo-EM reconstruction of the APC/C-MCC-Cdk2-cyclinA2-Cks2 comple... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4463 | |||||||||
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Title | Cryo-EM reconstruction of the APC/C-MCC-Cdk2-cyclinA2-Cks2 complex in the open conformation | |||||||||
![]() | sharpened map with B factor -30 | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Zhang S / Barford D | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 18.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.1 KB 32.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 162.5 KB | ||
Others | ![]() ![]() | 193.3 MB 193.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 356.9 KB | Display | ![]() |
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Full document | ![]() | 356 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4464C ![]() 4465C ![]() 4466C ![]() 4467C ![]() 6q6gC ![]() 6q6hC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map with B factor -30 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: halfmap1
File | emd_4463_half_map_1.map | ||||||||||||
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Annotation | halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap2
File | emd_4463_half_map_2.map | ||||||||||||
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Annotation | halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Cryo-EM reconstruction of the APC/C-MCC-Cdk2-cyclinA2-Cks2 comple...
+Supramolecule #1: Cryo-EM reconstruction of the APC/C-MCC-Cdk2-cyclinA2-Cks2 comple...
+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
+Macromolecule #19: BubR1
+Macromolecule #20: Mad2
+Macromolecule #21: Bub3
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 8 / Details: 20mM Hepes, 150mM NaCl, 0.5mM TCEP |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |