5BPT

Atomic-resolution structures of the APC/C subunits Apc4 and the Apc5 N-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain.

Cronin, N.B.Yang, J.Zhang, Z.Kulkarni, K.Chang, L.Yamano, H.Barford, D.

(2015) J Mol Biol 427: 3300-3315

  • DOI: https://doi.org/10.1016/j.jmb.2015.08.023
  • Primary Citation of Related Structures:  
    5BPT, 5BPW, 5BPZ

  • PubMed Abstract: 

    Many essential biological processes are mediated by complex molecular machines comprising multiple subunits. Knowledge on the architecture of individual subunits and their positions within the overall multimeric complex is key to understanding the molecular mechanisms of macromolecular assemblies. The anaphase-promoting complex/cyclosome (APC/C) is a large multisubunit complex that regulates cell cycle progression by ubiquitinating cell cycle proteins for proteolysis by the proteasome. The holo-complex is composed of 15 different proteins that assemble to generate a complex of 20 subunits. Here, we describe the crystal structures of Apc4 and the N-terminal domain of Apc5 (Apc5(N)). Apc4 comprises a WD40 domain split by a long α-helical domain, whereas Apc5(N) has an α-helical fold. In a separate study, we had fitted these atomic models to a 3.6-Å-resolution cryo-electron microscopy map of the APC/C. We describe how, in the context of the APC/C, regions of Apc4 disordered in the crystal assume order through contacts to Apc5, whereas Apc5(N) shows small conformational changes relative to its crystal structure. We discuss the complementary approaches of high-resolution electron microscopy and protein crystallography to the structure determination of subunits of multimeric complexes.


  • Organizational Affiliation

    Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MGC81278 protein741Xenopus laevisMutation(s): 0 
Gene Names: anapc4MGC81278
UniProt
Find proteins for Q6NU36 (Xenopus laevis)
Explore Q6NU36 
Go to UniProtKB:  Q6NU36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NU36
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.469α = 90
b = 90.469β = 90
c = 115.593γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC576/A14109

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary