3ZNH

Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

On Terminal Alkynes that Can React with Active-Site Cysteine Nucleophiles in Proteases.

Ekkebus, R.Van Kasteren, S.I.Kulathu, Y.Scholten, A.Berlin, I.Geurink, P.P.De Jong, A.Goerdayal, G.Neefjes, J.Heck, A.J.R.Komander, D.Ovaa, H.

(2013) J Am Chem Soc 135: 2867

  • DOI: 10.1021/ja309802n
  • Primary Citation of Related Structures:  
    3ZNH

  • PubMed Abstract: 
  • Active-site directed probes are powerful in studies of enzymatic function. We report an active-site directed probe based on a warhead so far considered unreactive. By replacing the C-terminal carboxylate of ubiquitin (Ub) with an alkyne functionality ...

    Active-site directed probes are powerful in studies of enzymatic function. We report an active-site directed probe based on a warhead so far considered unreactive. By replacing the C-terminal carboxylate of ubiquitin (Ub) with an alkyne functionality, a selective reaction with the active-site cysteine residue of de-ubiquitinating enzymes was observed. The resulting product was shown to be a quaternary vinyl thioether, as determined by X-ray crystallography. Proteomic analysis of proteins bound to an immobilized Ub alkyne probe confirmed the selectivity toward de-ubiquitinating enzymes. The observed reactivity is not just restricted to propargylated Ub, as highlighted by the selective reaction between caspase-1 (interleukin converting enzyme) and a propargylated peptide derived from IL-1β, a caspase-1 substrate.


    Organizational Affiliation

    Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN THIOESTERASEA183Crimean-Congo hemorrhagic fever virus strain IbAr10200Mutation(s): 0 
Gene Names: L
EC: 3.4.19.12 (PDB Primary Data), 2.7.7.48 (UniProt)
Find proteins for Q6TQR6 (Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970))
Explore Q6TQR6 
Go to UniProtKB:  Q6TQR6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
POLYUBIQUITIN-BB76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS  P0CG47
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.05α = 90
b = 146.05β = 90
c = 58.53γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references
  • Version 1.2: 2013-03-20
    Changes: Database references