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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ANAPHASE-PROMOTING COMPLEX SUBUNIT CUT9A, C [auth D]597Schizosaccharomyces pombeMutation(s): 0 
Find proteins for P41889 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P41889 
Go to UniProtKB:  P41889
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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 
Find proteins for O13916 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13916 
Go to UniProtKB:  O13916
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