+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10536 | |||||||||
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Title | SUMOylated apoAPC/C with repositioned APC2 WHB domain | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / 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 / 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 ...regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / 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 / 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 / Phosphorylation of the APC/C / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / mitotic metaphase chromosome alignment / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / positive regulation of axon extension / heterochromatin / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / 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 / mitotic spindle / spindle / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / 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 / cell cycle / cell division / negative regulation of gene expression / centrosome / ubiquitin protein ligase binding / nucleolus / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.78 Å | |||||||||
Authors | Barford D / Yatskevich S | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Cell Rep / Year: 2021 Title: Molecular mechanisms of APC/C release from spindle assembly checkpoint inhibition by APC/C SUMOylation. Authors: Stanislau Yatskevich / Jessie S Kroonen / Claudio Alfieri / Thomas Tischer / Anna C Howes / Linda Clijsters / Jing Yang / Ziguo Zhang / Kaige Yan / Alfred C O Vertegaal / David Barford / Abstract: The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that controls cell cycle transitions. Its regulation by the spindle assembly checkpoint (SAC) is coordinated with the ...The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that controls cell cycle transitions. Its regulation by the spindle assembly checkpoint (SAC) is coordinated with the attachment of sister chromatids to the mitotic spindle. APC/C SUMOylation on APC4 ensures timely anaphase onset and chromosome segregation. To understand the structural and functional consequences of APC/C SUMOylation, we reconstituted SUMOylated APC/C for electron cryo-microscopy and biochemical analyses. SUMOylation of the APC/C causes a substantial rearrangement of the WHB domain of APC/C's cullin subunit (APC2). Although APC/C SUMOylation results in a modest impact on normal APC/C activity, repositioning APC2 reduces the affinity of APC/C for the mitotic checkpoint complex (MCC), the effector of the SAC. This attenuates MCC-mediated suppression of APC/C activity, allowing for more efficient ubiquitination of APC/C substrates in the presence of the MCC. Thus, SUMOylation stimulates the reactivation of APC/C when the SAC is silenced, contributing to timely anaphase onset. | |||||||||
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_10536.map.gz | 14.2 MB | EMDB map data format | |
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Header (meta data) | emd-10536-v30.xml emd-10536.xml | 35.9 KB 35.9 KB | Display Display | EMDB header |
Images | emd_10536.png | 49.5 KB | ||
Others | emd_10536_additional_1.map.gz | 15.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10536 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10536 | HTTPS FTP |
-Related structure data
Related structure data | 6tntMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10536.map.gz / Format: CCP4 / Size: 147.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.085 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_10536_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : SUMOylated apoAPC/C with repositioned APC2 WHB domain
+Supramolecule #1: SUMOylated apoAPC/C with repositioned APC2 WHB domain
+Supramolecule #2: Body 2 with repositioned APC2 WHB domain after multi body refinement
+Supramolecule #3: Unidentified peptide
+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: UNIDENTIFIED PEPTIDE
+Macromolecule #15: Anaphase-promoting complex subunit 7
+Macromolecule #16: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.16 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.00) |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137954 |