2XPI

Crystal structure of APC/C hetero-tetramer Cut9-Hcn1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Literature

The Apc/C Subunit Cdc16/Cut9 is a Contiguous Tetratricopeptide Superhelix with a Homo-Dimer Interface Similar to Cdc27

Zhang, Z., Kulkarni, K.A., Hanrahan, S.J., Thompson, A.J., Barford, D.

(2010) EMBO J 29: 3733

  • DOI: 10.1038/emboj.2010.247
  • Primary Citation of Related Structures:  
    2XPI

  • PubMed Abstract: 

    • The anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase responsible for controlling cell cycle transitions, is a multisubunit complex assembled from 13 different proteins. Numerous APC/C subunits incorporate multiple copies of the tetratricopeptide repeat (TPR) ...

    The anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase responsible for controlling cell cycle transitions, is a multisubunit complex assembled from 13 different proteins. Numerous APC/C subunits incorporate multiple copies of the tetratricopeptide repeat (TPR). Here, we report the crystal structure of Schizosaccharomyces pombe Cut9 (Cdc16/Apc6) in complex with Hcn1 (Cdc26), showing that Cdc16/Cut9 is a contiguous TPR superhelix of 14 TPR units. A C-terminal block of TPR motifs interacts with Hcn1, whereas an N-terminal TPR block mediates Cdc16/Cut9 self-association through a homotypic interface. This dimer interface is structurally related to the N-terminal dimerization domain of Cdc27, demonstrating that both Cdc16/Cut9 and Cdc27 form homo-dimers through a conserved mechanism. The acetylated N-terminal Met residue of Hcn1 is enclosed within a chamber created from the Cut9 TPR superhelix. Thus, in complex with Cdc16/Cut9, the N-acetyl-Met residue of Hcn1, a putative degron for the Doa10 E3 ubiquitin ligase, is inaccessible for Doa10 recognition, protecting Hcn1/Cdc26 from ubiquitin-dependent degradation. This finding may provide a structural explanation for a mechanism to control the stoichiometry of proteins participating in multisubunit complexes.

    Organizational Affiliation: 

    Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT CUT9A,
C [auth D]		597Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P41889 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P41889 
Go to UniProtKB:  P41889
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41889
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT HCN1 HCN1/CDC26,20S CYCLOSOME/APC COMPLEX PROTEIN HCN1, CHAPERONE-LIKE PROTEIN HCN1, HIGH COPY SUPPRESSOR OF CUT9 PROTEIN 1B,
D [auth E]		81Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O13916 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13916 
Go to UniProtKB:  O13916
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13916
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AUC
Query on AUC
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth D],
H [auth D]		GOLD (I) CYANIDE ION
C2 Au N2
DGOHFTDNMSZWDQ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.4α = 90
b = 151.92β = 90.84
c = 91.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Other, Version format compliance
  • Version 1.2: 2019-04-03
    Changes: Advisory, Data collection, Derived calculations, Other, Source and taxonomy