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- EMDB-4028: Human Anaphase-Promoting Complex/Cyclosome (APC/C) APC15 deletion... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4028 | |||||||||
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Title | Human Anaphase-Promoting Complex/Cyclosome (APC/C) APC15 deletion mutant bound to Mitotic Checkpoint Complex (MCC) and the E2 UBE2C (aka UBCH10) poised for ubiquitination of MCC's CDC20 | |||||||||
![]() | Human Anaphase-Promoting Complex/Cyclosome (APC/C) APC15 deletion mutant bound to Mitotic Checkpoint Complex (MCC) and the E2 UBE2C (aka UBCH10) poised for ubiquitination of MCC's CDC20 | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 18.0 Å | |||||||||
![]() | Stark H / Schulman BA / Peters JM | |||||||||
![]() | ![]() Title: Cryo-EM of Mitotic Checkpoint Complex-Bound APC/C Reveals Reciprocal and Conformational Regulation of Ubiquitin Ligation. Authors: Masaya Yamaguchi / Ryan VanderLinden / Florian Weissmann / Renping Qiao / Prakash Dube / Nicholas G Brown / David Haselbach / Wei Zhang / Sachdev S Sidhu / Jan-Michael Peters / Holger Stark ...Authors: Masaya Yamaguchi / Ryan VanderLinden / Florian Weissmann / Renping Qiao / Prakash Dube / Nicholas G Brown / David Haselbach / Wei Zhang / Sachdev S Sidhu / Jan-Michael Peters / Holger Stark / Brenda A Schulman / ![]() ![]() ![]() ![]() Abstract: The mitotic checkpoint complex (MCC) coordinates proper chromosome biorientation on the spindle with ubiquitination activities of CDC20-activated anaphase-promoting complex/cyclosome (APC/C(CDC20)). ...The mitotic checkpoint complex (MCC) coordinates proper chromosome biorientation on the spindle with ubiquitination activities of CDC20-activated anaphase-promoting complex/cyclosome (APC/C(CDC20)). APC/C(CDC20) and two E2s, UBE2C and UBE2S, catalyze ubiquitination through distinct architectures for linking ubiquitin (UB) to substrates and elongating polyUB chains, respectively. MCC, which contains a second molecule of CDC20, blocks APC/C(CDC20)-UBE2C-dependent ubiquitination of Securin and Cyclins, while differentially determining or inhibiting CDC20 ubiquitination to regulate spindle surveillance, checkpoint activation, and checkpoint termination. Here electron microscopy reveals conformational variation of APC/C(CDC20)-MCC underlying this multifaceted regulation. MCC binds APC/C-bound CDC20 to inhibit substrate access. However, rotation about the CDC20-MCC assembly and conformational variability of APC/C modulate UBE2C-catalyzed ubiquitination of MCC's CDC20 molecule. Access of UBE2C is limiting for subsequent polyubiquitination by UBE2S. We propose that conformational dynamics of APC/C(CDC20)-MCC modulate E2 activation and determine distinctive ubiquitination activities as part of a response mechanism ensuring accurate sister chromatid segregation. | |||||||||
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 | ![]() | 2.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.7 KB 10.7 KB | Display Display | ![]() |
Images | ![]() | 91.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4021C ![]() 4022C ![]() 4023C ![]() 4024C ![]() 4025C ![]() 4026C ![]() 4027C ![]() 5khrC ![]() 5khuC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Human Anaphase-Promoting Complex/Cyclosome (APC/C) APC15 deletion mutant bound to Mitotic Checkpoint Complex (MCC) and the E2 UBE2C (aka UBCH10) poised for ubiquitination of MCC's CDC20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Human Anaphase-Promoting Complex/Cyclosome (APC/C) APC15 deletion...
Entire | Name: Human Anaphase-Promoting Complex/Cyclosome (APC/C) APC15 deletion mutant bound to Mitotic Checkpoint Complex (MCC) and the E2 UBE2C (aka UBCH10) poised for ubiquitination of MCC's CDC20 |
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Components |
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-Supramolecule #1: Human Anaphase-Promoting Complex/Cyclosome (APC/C) APC15 deletion...
Supramolecule | Name: Human Anaphase-Promoting Complex/Cyclosome (APC/C) APC15 deletion mutant bound to Mitotic Checkpoint Complex (MCC) and the E2 UBE2C (aka UBCH10) poised for ubiquitination of MCC's CDC20 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 1.5 MDa |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Staining | Type: NEGATIVE / Material: Uranyl Formate | ||||||||||||
Details | Grafix treated complex |
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Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Image recording | Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 160 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 120560 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
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Image processing
Particle selection | Number selected: 195939 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 25472 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |