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Yorodumi- EMDB-4023: Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Check... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4023 | |||||||||
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Title | Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Checkpoint Complex (APC/C-MCC) in a closed conformation. | |||||||||
Map data | Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Checkpoint Complex (APC/C-MCC) in a closed conformation | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Stark H / Schulman BA / Peters JM | |||||||||
Citation | Journal: Mol Cell / Year: 2016 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4023.map.gz | 5.7 MB | EMDB map data format | |
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Header (meta data) | emd-4023-v30.xml emd-4023.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_4023.png | 182.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4023 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4023 | HTTPS FTP |
-Related structure data
Related structure data | 4021C 4022C 4024C 4025C 4026C 4027C 4028C 5khrC 5khuC 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_4023.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Checkpoint Complex (APC/C-MCC) in a closed conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.57 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 : Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Check...
Entire | Name: Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Checkpoint Complex (APC/C-MCC) in a closed conformation. |
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Components |
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-Supramolecule #1: Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Check...
Supramolecule | Name: Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Checkpoint Complex (APC/C-MCC) in a closed conformation. type: complex / ID: 1 / Parent: 0 Details: Human Anaphase-Promoting Complex/Cyclosome bound to Mitotic Checkpoint Complex (APC/C-MCC) in a closed conformation. |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Tricoplusia ni (cabbage looper) / Recombinant plasmid: biGBac |
Molecular weight | Theoretical: 1.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | Grafix treated complex |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 0.0035 µm / Calibrated defocus min: 0.0007 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.001 mm / Nominal magnification: 94000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3254 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 433958 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 53143 |