4MDK

Cdc34-ubiquitin-CC0651 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6095 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin.

Huang, H., Ceccarelli, D.F., Orlicky, S., St-Cyr, D.J., Ziemba, A., Garg, P., Plamondon, S., Auer, M., Sidhu, S., Marinier, A., Kleiger, G., Tyers, M., Sicheri, F.

(2014) Nat.Chem.Biol. 10: 156-163

  • DOI: 10.1038/nchembio.1412

  • PubMed Abstract: 

    • Weak protein interactions between ubiquitin and the ubiquitin-proteasome system (UPS) enzymes that mediate its covalent attachment to substrates serve to position ubiquitin for optimal catalytic transfer. We show that a small-molecule inhibitor of th ...

    Weak protein interactions between ubiquitin and the ubiquitin-proteasome system (UPS) enzymes that mediate its covalent attachment to substrates serve to position ubiquitin for optimal catalytic transfer. We show that a small-molecule inhibitor of the E2 ubiquitin-conjugating enzyme Cdc34A, called CC0651, acts by trapping a weak interaction between ubiquitin and the E2 donor ubiquitin-binding site. A structure of the ternary CC0651-Cdc34A-ubiquitin complex reveals that the inhibitor engages a composite binding pocket formed from Cdc34A and ubiquitin. CC0651 also suppresses the spontaneous hydrolysis rate of the Cdc34A-ubiquitin thioester without decreasing the interaction between Cdc34A and the RING domain subunit of the E3 enzyme. Stabilization of the numerous other weak interactions between ubiquitin and UPS enzymes by small molecules may be a feasible strategy to selectively inhibit different UPS activities.

    Organizational Affiliation: 

    Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 R1
A, B, C, D
180Homo sapiensMutation(s): 0 
Gene Names: CDC34 (UBCH3, UBE2R1)
EC: 2.3.2.23
Find proteins for P49427 (Homo sapiens)
Go to Gene View: CDC34
Go to UniProtKB:  P49427
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
E, F, G, H
80Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U94
Query on U94
Download SDF File 
Download CCD File 
A, B, C, D
4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid
C20 H21 Cl2 N O6
NTCBTNCWNRCBGX-YTQUADARSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6095 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.403α = 71.89
b = 72.220β = 79.63
c = 75.912γ = 81.61
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
ADSCdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2014-02-05
    Type: Database references