[English] 日本語
Yorodumi- EMDB-4037: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4037 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 4.2 angstrom resolution | |||||||||
Map data | None | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information metaphase/anaphase transition of cell cycle / mitotic spindle assembly checkpoint MAD1-MAD2 complex / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic cell cycle spindle assembly checkpoint / regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / regulation of meiotic nuclear division ...metaphase/anaphase transition of cell cycle / mitotic spindle assembly checkpoint MAD1-MAD2 complex / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic cell cycle spindle assembly checkpoint / regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / regulation of meiotic nuclear division / positive regulation of synapse maturation / meiotic sister chromatid cohesion, centromeric / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / positive regulation of mitotic metaphase/anaphase transition / metaphase/anaphase transition of mitotic cell cycle / regulation of exit from mitosis / positive regulation of synaptic plasticity / nuclear pore nuclear basket / outer kinetochore / Phosphorylation of the APC/C / anaphase-promoting complex binding / protein localization to chromosome, centromeric region / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / negative regulation of ubiquitin protein ligase activity / mitotic sister chromatid cohesion / mitotic metaphase chromosome alignment / mitotic spindle assembly checkpoint signaling / regulation of mitotic cell cycle / mitotic sister chromatid segregation / cullin family protein binding / establishment of mitotic spindle orientation / Regulation of APC/C activators between G1/S and early anaphase / mitotic spindle assembly / negative regulation of mitotic cell cycle / Transcriptional Regulation by VENTX / positive regulation of axon extension / heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / brain development / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / negative regulation of protein catabolic process / spindle / mitotic spindle / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / spindle pole / ubiquitin-protein transferase activity / Separation of Sister Chromatids / ubiquitin protein ligase activity / microtubule cytoskeleton / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / cell differentiation / molecular adaptor activity / protein ubiquitination / non-specific serine/threonine protein kinase / Ub-specific processing proteases / protein kinase activity / cell cycle / cell division / phosphorylation / negative regulation of gene expression / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Alfieri C / Chang L / Zhang Z / Yang J / Maslen S / Skehel M / Barford D | |||||||||
Citation | Journal: Nature / Year: 2016 Title: Molecular basis of APC/C regulation by the spindle assembly checkpoint. Authors: Claudio Alfieri / Leifu Chang / Ziguo Zhang / Jing Yang / Sarah Maslen / Mark Skehel / David Barford / Abstract: In the dividing eukaryotic cell, the spindle assembly checkpoint (SAC) ensures that each daughter cell inherits an identical set of chromosomes. The SAC coordinates the correct attachment of sister ...In the dividing eukaryotic cell, the spindle assembly checkpoint (SAC) ensures that each daughter cell inherits an identical set of chromosomes. The SAC coordinates the correct attachment of sister chromatid kinetochores to the mitotic spindle with activation of the anaphase-promoting complex (APC/C), the E3 ubiquitin ligase responsible for initiating chromosome separation. In response to unattached kinetochores, the SAC generates the mitotic checkpoint complex (MCC), which inhibits the APC/C and delays chromosome segregation. By cryo-electron microscopy, here we determine the near-atomic resolution structure of a human APC/C–MCC complex (APC/C(MCC)). Degron-like sequences of the MCC subunit BubR1 block degron recognition sites on Cdc20, the APC/C coactivator subunit responsible for substrate interactions. BubR1 also obstructs binding of the initiating E2 enzyme UbcH10 to repress APC/C ubiquitination activity. Conformational variability of the complex enables UbcH10 association, and structural analysis shows how the Cdc20 subunit intrinsic to the MCC (Cdc20(MCC)) is ubiquitinated, a process that results in APC/C reactivation when the SAC is silenced. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4037.map.gz | 8.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4037-v30.xml emd-4037.xml | 41.4 KB 41.4 KB | Display Display | EMDB header |
Images | emd_4037_1.png emd_4037_2.png emd_4037_3.png emd_4037_4.png | 76 KB 196.4 KB 185.1 KB 216.3 KB | ||
Others | emd_4037_additional_1.map.gz emd_4037_additional_2.map.gz emd_4037_additional_3.map.gz | 33.5 MB 7.8 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4037 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4037 | HTTPS FTP |
-Related structure data
Related structure data | 5lcwMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4037.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: None
File | emd_4037_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: None
File | emd_4037_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: None
File | emd_4037_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Anaphase-promoting complex/Cyclosome, in complex with the Mitotic...
+Supramolecule #1: Anaphase-promoting complex/Cyclosome, in complex with the Mitotic...
+Macromolecule #1: Anaphase-promoting complex subunit 1
+Macromolecule #2: Anaphase-promoting complex subunit 11
+Macromolecule #3: Cell division cycle protein 23 homolog
+Macromolecule #4: Anaphase-promoting complex subunit 15
+Macromolecule #5: Anaphase-promoting complex subunit 16
+Macromolecule #6: Cell division cycle protein 27 homolog
+Macromolecule #7: Anaphase-promoting complex subunit CDC26
+Macromolecule #8: Anaphase-promoting complex subunit 4
+Macromolecule #9: Cell division cycle protein 16 homolog
+Macromolecule #10: Anaphase-promoting complex subunit 10
+Macromolecule #11: Anaphase-promoting complex subunit 13
+Macromolecule #12: Anaphase-promoting complex subunit 2
+Macromolecule #13: Anaphase-promoting complex subunit 5
+Macromolecule #14: Cell division cycle protein 20 homolog
+Macromolecule #15: Cell division cycle protein 20 homolog
+Macromolecule #16: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta,Mito...
+Macromolecule #17: Anaphase-promoting complex subunit 7
+Macromolecule #18: Mitotic spindle assembly checkpoint protein MAD2A
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 27.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
---|---|
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 155263 |