Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 29416.27 
• Atom Count: 1774 
• Residue Count: 259 
• Unique protein chains: 2

3ZNH

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

• DOI: 10.2210/pdb3ZNH/pdb

• Classification: HYDROLASE/SIGNALING PROTEIN
• Organism(s): Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970), Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): 1 


• 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: 2.3 Å
• R-Value Free: 0.275 
• R-Value Work: 0.211 

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


• 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

Find similar proteins by: Sequence  |  Structure

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
POLYUBIQUITIN-B	B	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AYE	B	NON-POLYMER	C3 H7 N		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.275 
• R-Value Work: 0.211 
• Space Group: P 6₂ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 146.050	α = 90.00
b = 146.050	β = 90.00
c = 58.530	γ = 120.00

Software Package:

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

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
  Type: Database references
• Version 1.2: 2013-03-20
  Type: Database references