5G05 | pdb_00005g05

Cryo-EM structure of combined apo phosphorylated APC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Molecular Mechanism of Apc/C Activation by Mitotic Phosphorylation.

Zhang, S.Chang, L.Alfieri, C.Zhang, Z.Yang, J.Maslen, S.Skehel, M.Barford, D.

(2016) Nature 533: 260

  • DOI: https://doi.org/10.1038/nature17973
  • Primary Citation of Related Structures:  
    5G04, 5G05

  • PubMed Abstract: 

    In eukaryotes, the anaphase-promoting complex (APC/C, also known as the cyclosome) regulates the ubiquitin-dependent proteolysis of specific cell-cycle proteins to coordinate chromosome segregation in mitosis and entry into the G1 phase. The catalytic activity of the APC/C and its ability to specify the destruction of particular proteins at different phases of the cell cycle are controlled by its interaction with two structurally related coactivator subunits, Cdc20 and Cdh1. Coactivators recognize substrate degrons, and enhance the affinity of the APC/C for its cognate E2 (refs 4-6). During mitosis, cyclin-dependent kinase (Cdk) and polo-like kinase (Plk) control Cdc20- and Cdh1-mediated activation of the APC/C. Hyperphosphorylation of APC/C subunits, notably Apc1 and Apc3, is required for Cdc20 to activate the APC/C, whereas phosphorylation of Cdh1 prevents its association with the APC/C. Since both coactivators associate with the APC/C through their common C-box and Ile-Arg tail motifs, the mechanism underlying this differential regulation is unclear, as is the role of specific APC/C phosphorylation sites. Here, using cryo-electron microscopy and biochemical analysis, we define the molecular basis of how phosphorylation of human APC/C allows for its control by Cdc20. An auto-inhibitory segment of Apc1 acts as a molecular switch that in apo unphosphorylated APC/C interacts with the C-box binding site and obstructs engagement of Cdc20. Phosphorylation of the auto-inhibitory segment displaces it from the C-box-binding site. Efficient phosphorylation of the auto-inhibitory segment, and thus relief of auto-inhibition, requires the recruitment of Cdk-cyclin in complex with a Cdk regulatory subunit (Cks) to a hyperphosphorylated loop of Apc3. We also find that the small-molecule inhibitor, tosyl-l-arginine methyl ester, preferentially suppresses APC/C(Cdc20) rather than APC/C(Cdh1), and interacts with the binding sites of both the C-box and Ile-Arg tail motifs. Our results reveal the mechanism for the regulation of mitotic APC/C by phosphorylation and provide a rationale for the development of selective inhibitors of this state.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 11,944Homo sapiensMutation(s): 0 
Gene Names: ANAPC1TSG24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1A4 (Homo sapiens)
Explore Q9H1A4 
Go to UniProtKB:  Q9H1A4
PHAROS:  Q9H1A4
GTEx:  ENSG00000153107 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1A4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 1184Homo sapiensMutation(s): 0 
Gene Names: ANAPC11HSPC214
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYG5 (Homo sapiens)
Explore Q9NYG5 
Go to UniProtKB:  Q9NYG5
PHAROS:  Q9NYG5
GTEx:  ENSG00000141552 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX2 (Homo sapiens)
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Go to UniProtKB:  Q9UJX2
PHAROS:  Q9UJX2
GTEx:  ENSG00000094880 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJX2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 15121Homo sapiensMutation(s): 0 
Gene Names: ANAPC15C11ORF51HSPC020
UniProt & NIH Common Fund Data Resources
Find proteins for P60006 (Homo sapiens)
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PHAROS:  P60006
GTEx:  ENSG00000110200 
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UniProt GroupP60006
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 16110Homo sapiensMutation(s): 0 
Gene Names: ANAPC16C10ORF104
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DE5 (Homo sapiens)
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PHAROS:  Q96DE5
GTEx:  ENSG00000166295 
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UniProt GroupQ96DE5
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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
UniProt & NIH Common Fund Data Resources
Find proteins for P30260 (Homo sapiens)
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PHAROS:  P30260
GTEx:  ENSG00000004897 
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UniProt GroupP30260
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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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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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 4808Homo sapiensMutation(s): 0 
Gene Names: ANAPC4APC4
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Find proteins for Q9UJX5 (Homo sapiens)
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PHAROS:  Q9UJX5
GTEx:  ENSG00000053900 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJX5
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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
UniProt & NIH Common Fund Data Resources
Find proteins for Q13042 (Homo sapiens)
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PHAROS:  Q13042
GTEx:  ENSG00000130177 
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UniProt GroupQ13042
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 10185Homo sapiensMutation(s): 0 
Gene Names: ANAPC10APC10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM13 (Homo sapiens)
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PHAROS:  Q9UM13
GTEx:  ENSG00000164162 
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UniProt GroupQ9UM13
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 1374Bos taurusMutation(s): 0 
Gene Names: ANAPC13
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 2822Homo sapiensMutation(s): 0 
Gene Names: ANAPC2APC2KIAA1406
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX6 (Homo sapiens)
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PHAROS:  Q9UJX6
GTEx:  ENSG00000176248 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJX6
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT 5755Homo sapiensMutation(s): 0 
Gene Names: ANAPC5APC5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX4 (Homo sapiens)
Explore Q9UJX4 
Go to UniProtKB:  Q9UJX4
PHAROS:  Q9UJX4
GTEx:  ENSG00000089053 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJX4
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
UNIDENTIFIED PEPTIDEQ [auth T]15unidentifiedMutation(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
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX3 (Homo sapiens)
Explore Q9UJX3 
Go to UniProtKB:  Q9UJX3
PHAROS:  Q9UJX3
GTEx:  ENSG00000196510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJX3
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Other, Refinement description
  • Version 2.0: 2019-09-11
    Changes: Advisory, Atomic model, Data collection
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
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