6TM5

Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Nek2A substrate at 3.9 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A unique binding mode of Nek2A to the APC/C allows its ubiquitination during prometaphase.

Alfieri, C.Tischer, T.Barford, D.

(2020) EMBO Rep 21: e49831-e49831

  • DOI: https://doi.org/10.15252/embr.201949831
  • Primary Citation of Related Structures:  
    6TLJ, 6TM5

  • PubMed 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 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 MCC ) 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.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 11,944Homo sapiensMutation(s): 0 
Gene Names: ANAPC1TSG24
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PHAROS:  Q9H1A4
GTEx:  ENSG00000153107 
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UniProt GroupQ9H1A4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 1184Homo sapiensMutation(s): 0 
Gene Names: ANAPC11HSPC214
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PHAROS:  Q9NYG5
GTEx:  ENSG00000141552 
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UniProt GroupQ9NYG5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 23 homolog
C, P
597Homo sapiensMutation(s): 0 
Gene Names: CDC23ANAPC8
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PHAROS:  Q9UJX2
GTEx:  ENSG00000094880 
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UniProt GroupQ9UJX2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 15121Homo sapiensMutation(s): 0 
Gene Names: ANAPC15C11orf51HSPC020
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GTEx:  ENSG00000110200 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 16110Homo sapiensMutation(s): 0 
Gene Names: ANAPC16C10orf104CENP-27
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GTEx:  ENSG00000166295 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 27 homolog
F, H
824Homo sapiensMutation(s): 0 
Gene Names: CDC27ANAPC3D0S1430ED17S978E
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Find proteins for P30260 (Homo sapiens)
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GTEx:  ENSG00000004897 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit CDC26G,
R [auth W]
85Homo sapiensMutation(s): 0 
Gene Names: CDC26ANAPC12C9orf17
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GTEx:  ENSG00000176386 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 4808Homo sapiensMutation(s): 0 
Gene Names: ANAPC4APC4
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GTEx:  ENSG00000053900 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 16 homolog
J, K
620Homo sapiensMutation(s): 0 
Gene Names: CDC16ANAPC6
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GTEx:  ENSG00000130177 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 10185Homo sapiensMutation(s): 0 
Gene Names: ANAPC10APC10
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GTEx:  ENSG00000164162 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 1374Homo sapiensMutation(s): 0 
Gene Names: ANAPC13
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GTEx:  ENSG00000129055 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 2822Homo sapiensMutation(s): 0 
Gene Names: ANAPC2APC2KIAA1406
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GTEx:  ENSG00000176248 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 5755Homo sapiensMutation(s): 0 
Gene Names: ANAPC5APC5
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GTEx:  ENSG00000089053 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Apc1 loopQ [auth T]15Homo sapiensMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 7S [auth X],
T [auth Y]
599Homo sapiensMutation(s): 0 
Gene Names: ANAPC7APC7
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GTEx:  ENSG00000196510 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Nek2U [auth S]445Homo sapiensMutation(s): 0 
Gene Names: NEK2NEK2ANLK1
EC: 2.7.11.1
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Find proteins for P51955 (Homo sapiens)
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GTEx:  ENSG00000117650 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Nek2V [auth Q]445Homo sapiensMutation(s): 0 
Gene Names: NEK2NEK2ANLK1
EC: 2.7.11.1
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GTEx:  ENSG00000117650 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UK--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2020-06-17
    Changes: Database references