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

    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.,1] Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA [2] Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China (W.T.); Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA (K.L.P.); Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA (F.S.).,Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA.,1] Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA [2].,1] Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA [2] Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China (W.T.); Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA (K.L.P.); Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA (F.S.). [3].,1] Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA [2] Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815, USA.,Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA.




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