- EMDB-10518: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in... -
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Basic information
Entry
Database: EMDB / ID: EMD-10518
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
Complex: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution
Protein or peptide: x 17 types
Ligand: x 1 types
Function / homology
Function and homology information
negative regulation of centriole-centriole cohesion / centrosome separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / 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 / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / 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 / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of synaptic plasticity / regulation of exit from mitosis / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition / 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 / positive regulation of telomere capping / Regulation of APC/C activators between G1/S and early anaphase / cullin family protein binding / 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 / : / Recruitment of NuMA to mitotic centrosomes / positive regulation of telomere maintenance via telomerase / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / AURKA Activation by TPX2 / nuclear periphery / meiotic cell cycle / condensed nuclear chromosome / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / chromosome segregation / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / brain development / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / kinetochore / spindle pole / spindle / Separation of Sister Chromatids / ubiquitin-protein transferase activity / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / mitotic cell cycle / midbody / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / microtubule / protein autophosphorylation / molecular adaptor activity / cell differentiation / non-specific serine/threonine protein kinase / protein kinase activity / protein ubiquitination / cell cycle / cell division / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / nucleolus / protein-containing complex / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
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
Deposition
Dec 3, 2019
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Header (metadata) release
Feb 5, 2020
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Map release
Feb 19, 2020
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Update
Dec 2, 2020
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Current status
Dec 2, 2020
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Entire : Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in...
Entire
Name: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution
Components
Complex: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution
Protein or peptide: Anaphase-promoting complex subunit 1
Protein or peptide: Anaphase-promoting complex subunit 11
Protein or peptide: Cell division cycle protein 23 homolog
Protein or peptide: Anaphase-promoting complex subunit 15
Protein or peptide: Anaphase-promoting complex subunit 16
Protein or peptide: Cell division cycle protein 27 homolog
Protein or peptide: Anaphase-promoting complex subunit CDC26
Protein or peptide: Anaphase-promoting complex subunit 4
Protein or peptide: Cell division cycle protein 16 homolog
Protein or peptide: Anaphase-promoting complex subunit 10
Protein or peptide: Anaphase-promoting complex subunit 13
Protein or peptide: Anaphase-promoting complex subunit 2
Protein or peptide: Anaphase-promoting complex subunit 5
Protein or peptide: Apc1 loop
Protein or peptide: Anaphase-promoting complex subunit 7
Protein or peptide: Serine/threonine-protein kinase Nek2
Protein or peptide: Serine/threonine-protein kinase Nek2
Ligand: ZINC ION
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Supramolecule #1: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in...
Supramolecule
Name: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
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