4N14

Crystal structure of Cdc20 and apcin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/nature13660
  • Primary Citation of Related Structures:  
    4N14

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 20 homolog314Homo sapiensMutation(s): 0 
Gene Names: CDC20
UniProt & NIH Common Fund Data Resources
Find proteins for Q12834 (Homo sapiens)
Explore Q12834 
Go to UniProtKB:  Q12834
PHAROS:  Q12834
GTEx:  ENSG00000117399 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12834
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WR7
Query on WR7

Download Ideal Coordinates CCD File 
B [auth A]2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl [(1R)-2,2,2-trichloro-1-(pyrimidin-2-ylamino)ethyl]carbamate
C13 H14 Cl3 N7 O4
ZEXHXVOGJFGTRX-SNVBAGLBSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
WR7 Binding MOAD:  4N14 Ki: 2.30e+4 (nM) from 1 assay(s)
BindingDB:  4N14 Kd: 1.23e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.041α = 90
b = 87.177β = 112.72
c = 48.043γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references
  • Version 1.2: 2014-11-05
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations