8PKP

Cryo-EM structure of the apo Anaphase-promoting complex/cyclosome (APC/C) at 3.2 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Cryo-EM structures of apo-APC/C and APC/C CDH1:EMI1 complexes provide insights into APC/C regulation.

Hofler, A.Yu, J.Yang, J.Zhang, Z.Chang, L.McLaughlin, S.H.Grime, G.W.Garman, E.F.Boland, A.Barford, D.

(2024) Nat Commun 15: 10074-10074

  • DOI: https://doi.org/10.1038/s41467-024-54398-5
  • Primary Citation of Related Structures:  
    8PKP, 9GAW

  • PubMed Abstract: 

    APC/C is a multi-subunit complex that functions as a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle regulatory proteins for degradation. The APC/C itself is regulated by the sequential action of its coactivator subunits CDC20 and CDH1, post-translational modifications, and its inhibitory binding partners EMI1 and the mitotic checkpoint complex. In this study, we took advantage of developments in cryo-electron microscopy to determine the structures of human APC/C CDH1:EMI1 and apo-APC/C at 2.9 Å and 3.2 Å resolution, respectively, providing insights into the regulation of APC/C activity. The high-resolution maps allow the unambiguous assignment of an α-helix to the N-terminus of CDH1 (CDH1 α1 ) in the APC/C CDH1:EMI1 ternary complex. We also identify a zinc-binding module in APC2 that confers structural stability to the complex, and we confirm the presence of zinc ions experimentally. Finally, due to the higher resolution and well defined density of these maps, we are able to build, aided by AlphaFold predictions, several intrinsically disordered regions in different APC/C subunits that likely play a role in proper APC/C assembly and regulation of its activity.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.


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 15B [auth D]121Homo sapiensMutation(s): 0 
Gene Names: ANAPC15C11orf51HSPC020
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PHAROS:  P60006
GTEx:  ENSG00000110200 
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UniProt GroupP60006
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit CDC26C [auth G],
N [auth W]
85Homo sapiensMutation(s): 0 
Gene Names: CDC26ANAPC12C9orf17
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Find proteins for Q8NHZ8 (Homo sapiens)
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PHAROS:  Q8NHZ8
GTEx:  ENSG00000176386 
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UniProt GroupQ8NHZ8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 16D [auth H]110Homo sapiensMutation(s): 0 
Gene Names: ANAPC16C10orf104CENP-27
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GTEx:  ENSG00000166295 
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UniProt GroupQ96DE5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 27 homologE [auth J],
J [auth P]
824Homo sapiensMutation(s): 0 
Gene Names: CDC27ANAPC3D0S1430ED17S978E
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GTEx:  ENSG00000004897 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 16 homologF [auth K],
K [auth Q]
620Homo sapiensMutation(s): 0 
Gene Names: CDC16ANAPC6
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Find proteins for Q13042 (Homo sapiens)
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PHAROS:  Q13042
GTEx:  ENSG00000130177 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 10G [auth L]185Homo sapiensMutation(s): 0 
Gene Names: ANAPC10APC10
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PHAROS:  Q9UM13
GTEx:  ENSG00000164162 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 13H [auth M]74Homo sapiensMutation(s): 0 
Gene Names: ANAPC13
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PHAROS:  Q9BS18
GTEx:  ENSG00000129055 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 5I [auth O]755Homo sapiensMutation(s): 0 
Gene Names: ANAPC5APC5
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GTEx:  ENSG00000089053 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 23 homologL [auth U],
M [auth V]
597Homo sapiensMutation(s): 0 
Gene Names: CDC23ANAPC8
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GTEx:  ENSG00000094880 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 7O [auth Y],
P [auth Z]
565Homo sapiensMutation(s): 0 
Gene Names: ANAPC7APC7
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GTEx:  ENSG00000196510 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 4Q [auth I]814Homo sapiensMutation(s): 0 
Gene Names: ANAPC4APC4
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GTEx:  ENSG00000053900 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 2R [auth N]822Homo sapiensMutation(s): 0 
Gene Names: ANAPC2APC2KIAA1406
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PHAROS:  Q9UJX6
GTEx:  ENSG00000176248 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 11S [auth C]84Homo sapiensMutation(s): 0 
Gene Names: ANAPC11HSPC214
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Find proteins for Q9NYG5 (Homo sapiens)
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PHAROS:  Q9NYG5
GTEx:  ENSG00000141552 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16-3549
MODEL REFINEMENTCoot0.9
RECONSTRUCTIONcryoSPARC2.14.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_185235
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/6

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 2.0: 2024-08-07
    Type: Coordinate replacement
    Reason: Atoms with unrealistic or zero occupancies
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 2.2: 2025-01-29
    Changes: Data collection, Database references