Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.42 kDa 
• Atom Count: 1822 
• Modelled Residue Count: 229 
• Deposited Residue Count: 259 
• Unique protein chains: 2

3ZNH

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

• PDB DOI: 10.2210/pdb3ZNH/pdb

• Classification: HYDROLASE/SIGNALING PROTEIN
• Organism(s): Crimean-Congo hemorrhagic fever virus strain IbAr10200, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-02-14 Released: 2013-02-27 
• Deposition Author(s): Ekkebus, R., vanKasteren, S.I., Kulathu, Y., Scholten, A., Berlin, I., deJong, A., Goerdayal, G., Neefjes, J., Heck, A.J.R., Komander, D., Ovaa, H.

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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 

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

• PubMed: 23387960 
• 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, 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN THIOESTERASE	A	183	Crimean-Congo hemorrhagic fever virus strain IbAr10200	Mutation(s): 0  Gene Names: L EC: 3.4.19.12 (PDB Primary Data), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q6TQR6 (Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)) Explore Q6TQR6  Go to UniProtKB:  Q6TQR6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYUBIQUITIN-B	B	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

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 = 146.05	α = 90
b = 146.05	β = 90
c = 58.53	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-14 
• Released Date: 2013-02-27 
Deposition Author(s): Ekkebus, R., vanKasteren, S.I., Kulathu, Y., Scholten, A., Berlin, I., deJong, A., Goerdayal, G., Neefjes, J., Heck, A.J.R., Komander, D., Ovaa, H.

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