› 3znh

X-ray diffraction
2.3Å resolution

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

Released:
DOI: 10.2210/pdb3znh/pdb
PDB entry 3znh coloured by chain, front view.
PDB entry 3znh coloured by chain, side view.
PDB entry 3znh coloured by chain, top view.
Source organisms:
Primary publication:
On terminal alkynes that can react with active-site cysteine nucleophiles in proteases.
Ekkebus R, van Kasteren SI, Kulathu Y, Scholten A, Berlin I, Geurink PP, de Jong A, Goerdayal S, Neefjes J, Heck AJ, Komander D, Ovaa H
J Am Chem Soc 135 2867-70 (2013)
PMID: 23387960

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143279 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
RNA-directed RNA polymerase L Chain: A
Molecule details ›
Chain: A
Length: 183 amino acids
Theoretical weight: 20.86 KDa
Source organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q6TQR6 (Residues: 1-183; Coverage: 5%)
Gene name: L
Sequence domains: OTU-like cysteine protease
Structure domains: Cathepsin B; Chain A
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P6222
Unit cell:
a: 146.05Å b: 146.05Å c: 58.53Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.214 0.211 0.275
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

29 review citations

Activity-based profiling of proteases.
Sanman et al. (2014)
28 more

4 mentions without citation

Structure and Function of Viral Deubiquitinating Enzymes.
Bailey-Elkin et al. (2017)
3 more