4N14

Crystal structure of Cdc20 and apcin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synergistic blockade of mitotic exit by two chemical inhibitors of the APC/C.

Sackton, K.L.Dimova, N.Zeng, X.Tian, W.Zhang, M.Sackton, T.B.Meaders, J.Pfaff, K.L.Sigoillot, F.Yu, H.Luo, X.King, R.W.

(2014) Nature 514: 646-649

  • DOI: 10.1038/nature13660

  • PubMed Abstract: 
  • Protein machines are multi-subunit protein complexes that orchestrate highly regulated biochemical tasks. An example is the anaphase-promoting complex/cyclosome (APC/C), a 13-subunit ubiquitin ligase that initiates the metaphase-anaphase transition a ...

    Protein machines are multi-subunit protein complexes that orchestrate highly regulated biochemical tasks. An example is the anaphase-promoting complex/cyclosome (APC/C), a 13-subunit ubiquitin ligase that initiates the metaphase-anaphase transition and mitotic exit by targeting proteins such as securin and cyclin B1 for ubiquitin-dependent destruction by the proteasome. Because blocking mitotic exit is an effective approach for inducing tumour cell death, the APC/C represents a potential novel target for cancer therapy. APC/C activation in mitosis requires binding of Cdc20 (ref. 5), which forms a co-receptor with the APC/C to recognize substrates containing a destruction box (D-box). Here we demonstrate that we can synergistically inhibit APC/C-dependent proteolysis and mitotic exit by simultaneously disrupting two protein-protein interactions within the APC/C-Cdc20-substrate ternary complex. We identify a small molecule, called apcin (APC inhibitor), which binds to Cdc20 and competitively inhibits the ubiquitylation of D-box-containing substrates. Analysis of the crystal structure of the apcin-Cdc20 complex suggests that apcin occupies the D-box-binding pocket on the side face of the WD40-domain. The ability of apcin to block mitotic exit is synergistically amplified by co-addition of tosyl-l-arginine methyl ester, a small molecule that blocks the APC/C-Cdc20 interaction. This work suggests that simultaneous disruption of multiple, weak protein-protein interactions is an effective approach for inactivating a protein machine.


    Related Citations: 
    • Cdc20: a WD40 activator for a cell cycle degradation machine.
      Yu, H.
      (2007) Mol.Cell 27: 3


    Organizational Affiliation

    1] Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle protein 20 homolog
A
314Homo sapiensMutation(s): 0 
Gene Names: CDC20
Find proteins for Q12834 (Homo sapiens)
Go to Gene View: CDC20
Go to UniProtKB:  Q12834
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WR7
Query on WR7

Download SDF File 
Download CCD File 
A
2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl [(1R)-2,2,2-trichloro-1-(pyrimidin-2-ylamino)ethyl]carbamate
apcin
C13 H14 Cl3 N7 O4
ZEXHXVOGJFGTRX-SNVBAGLBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WR7Ki: 23000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.041α = 90.00
b = 87.177β = 112.72
c = 48.043γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-3000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-3000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-03 
  • Released Date: 2014-08-20 
  • Deposition Author(s): Luo, X., Tian, W., Yu, H.

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references
  • Version 1.2: 2014-11-05
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description