6TM5 image
Deposition Date 2019-12-03
Release Date 2020-02-19
Last Version Date 2024-10-23
Entry Detail
PDB ID:
6TM5
Keywords:
Title:
Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 1
Gene (Uniprot):ANAPC1
Chain IDs:A
Chain Length:1944
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 11
Gene (Uniprot):ANAPC11
Chain IDs:B
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Cell division cycle protein 23 homolog
Gene (Uniprot):CDC23
Chain IDs:C, P
Chain Length:597
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 15
Gene (Uniprot):ANAPC15
Chain IDs:D
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 16
Gene (Uniprot):ANAPC16
Chain IDs:E
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Cell division cycle protein 27 homolog
Gene (Uniprot):CDC27
Chain IDs:F, H
Chain Length:824
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit CDC26
Gene (Uniprot):CDC26
Chain IDs:G, R (auth: W)
Chain Length:85
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 4
Gene (Uniprot):ANAPC4
Chain IDs:I
Chain Length:808
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Cell division cycle protein 16 homolog
Gene (Uniprot):CDC16
Chain IDs:J, K
Chain Length:620
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 10
Gene (Uniprot):ANAPC10
Chain IDs:L
Chain Length:185
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 13
Gene (Uniprot):ANAPC13
Chain IDs:M
Chain Length:74
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 2
Gene (Uniprot):ANAPC2
Chain IDs:N
Chain Length:822
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 5
Gene (Uniprot):ANAPC5
Chain IDs:O
Chain Length:755
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein kinase Nek2
Gene (Uniprot):NEK2
Chain IDs:V (auth: Q)
Chain Length:445
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein kinase Nek2
Gene (Uniprot):NEK2
Chain IDs:U (auth: S)
Chain Length:445
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Apc1 loop
Chain IDs:Q (auth: T)
Chain Length:15
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Anaphase-promoting complex subunit 7
Gene (Uniprot):ANAPC7
Chain IDs:S (auth: X), T (auth: Y)
Chain Length:599
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
A unique binding mode of Nek2A to the APC/C allows its ubiquitination during prometaphase.
Embo Rep. 21 e49831 e49831 (2020)
PMID: 32307883 DOI: 10.15252/embr.201949831

Abstact

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/CMCC) 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.

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