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Yorodumi- EMDB-10518: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10518 | |||||||||
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Title | Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution | |||||||||
Map data | APC/C core complex in complex with Nek2A after 3D multi body refinement. Reconstruction for Nek2A MR1 | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of centriole-centriole cohesion / centrosome separation / 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 / regulation of attachment of spindle microtubules to kinetochore / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects ...negative regulation of centriole-centriole cohesion / centrosome separation / 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 / regulation of attachment of spindle microtubules to kinetochore / 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 / regulation of mitotic centrosome separation / enzyme-substrate adaptor activity / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / regulation of mitotic nuclear division / mitotic metaphase chromosome alignment / cullin family protein binding / positive regulation of telomere capping / Regulation of APC/C activators between G1/S and early anaphase / blastocyst development / Transcriptional Regulation by VENTX / mitotic spindle assembly / spindle assembly / positive regulation of axon extension / heterochromatin / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of telomerase activity / Recruitment of NuMA to mitotic centrosomes / positive regulation of telomere maintenance via telomerase / APC/C:Cdc20 mediated degradation of Cyclin B / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / AURKA Activation by TPX2 / meiotic cell cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / condensed nuclear chromosome / chromosome segregation / 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 / spindle pole / ubiquitin-protein transferase activity / Separation of Sister Chromatids / ubiquitin protein ligase activity / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / midbody / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / microtubule / protein autophosphorylation / cell differentiation / molecular adaptor activity / protein ubiquitination / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / nucleolus / protein-containing complex / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Alfieri C / Barford D | |||||||||
Funding support | 1 items
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Citation | Journal: EMBO Rep / Year: 2020 Title: A unique binding mode of Nek2A to the APC/C allows its ubiquitination during prometaphase. Authors: Claudio Alfieri / Thomas Tischer / David Barford / Abstract: The anaphase-promoting complex (APC/C) is the key E3 ubiquitin ligase which directs mitotic progression and exit by catalysing the sequential ubiquitination of specific substrates. The activity of ...The anaphase-promoting complex (APC/C) is the key E3 ubiquitin ligase which directs mitotic progression and exit by catalysing the sequential ubiquitination of specific substrates. The activity of the APC/C in mitosis is restrained by the spindle assembly checkpoint (SAC), which coordinates chromosome segregation with the assembly of the mitotic spindle. The SAC effector is the mitotic checkpoint complex (MCC), which binds and inhibits the APC/C. It is incompletely understood how the APC/C switches substrate specificity in a cell cycle-specific manner. For instance, it is unclear how in prometaphase, when APC/C activity towards cyclin B and securin is repressed by the MCC, the kinase Nek2A is ubiquitinated. Here, we combine biochemical and structural analysis with functional studies in cells to show that Nek2A is a conformational-specific binder of the APC/C-MCC complex (APC/C ) and that, in contrast to cyclin A, Nek2A can be ubiquitinated efficiently by the APC/C in conjunction with both the E2 enzymes UbcH10 and UbcH5. We propose that these special features of Nek2A allow its prometaphase-specific ubiquitination. | |||||||||
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_10518.map.gz | 12.2 MB | EMDB map data format | |
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Header (meta data) | emd-10518-v30.xml emd-10518.xml | 39.3 KB 39.3 KB | Display Display | EMDB header |
Images | emd_10518.png | 73.9 KB | ||
Others | emd_10518_additional_1.map.gz emd_10518_additional_2.map.gz emd_10518_additional_3.map.gz | 14.7 MB 6.5 MB 10.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10518 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10518 | HTTPS FTP |
-Related structure data
Related structure data | 6tm5MC 6tljC 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_10518.map.gz / Format: CCP4 / Size: 147.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | APC/C core complex in complex with Nek2A after 3D multi body refinement. Reconstruction for Nek2A MR1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: APC/C-Nek2A complex WHB domain
File | emd_10518_additional_1.map | ||||||||||||
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Annotation | APC/C-Nek2A complex WHB domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: APC/C-Nek2A complex WHB domain Polara data
File | emd_10518_additional_2.map | ||||||||||||
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Annotation | APC/C-Nek2A complex WHB domain Polara data | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: APC/C-Nek2A complex MR2
File | emd_10518_additional_3.map | ||||||||||||
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Annotation | APC/C-Nek2A complex MR2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in...
+Supramolecule #1: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in...
+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: Apc1 loop
+Macromolecule #15: Anaphase-promoting complex subunit 7
+Macromolecule #16: Serine/threonine-protein kinase Nek2
+Macromolecule #17: Serine/threonine-protein kinase Nek2
+Macromolecule #18: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 29.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 233840 |