› 3p06

X-ray diffraction
2.1Å resolution

Crystal structure of Tellina virus 1 VP4 protease in the form of an intra-molecular(cis)acyl-enzyme complex.

Released:
DOI: 10.2210/pdb3p06/pdb
PDB entry 3p06 coloured by chain, front view.
PDB entry 3p06 coloured by chain, side view.
PDB entry 3p06 coloured by chain, top view.
Source organism: Tellina virus 1
Primary publication:
Crystal structure of a viral protease intramolecular acyl-enzyme complex: insights into cis-cleavage at the VP4/VP3 junction of Tellina birnavirus.
Chung IY, Paetzel M
J Biol Chem 286 12475-82 (2011)
PMID: 21288899

Function and Biology Details

Reaction catalysed: 
Cleaves the (Ser/Thr)-Xaa-Ala-|-(Ser/Ala)-Gly motif in the polyprotein NH(2)-pVP2-VP4-VP3-COOH of infectious pancreatic necrosis virus at the pVP2-VP4 and VP4-VP3 junctions
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-173863 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
VP4 protein Chain: A
Molecule details ›
Chain: A
Length: 194 amino acids
Theoretical weight: 20.56 KDa
Source organism: Tellina virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q2PBR5 (Residues: 637-830; Coverage: 17%)
Sequence domains: Birnavirus VP4 protein
Structure domains: Ribosomal Protein S5; domain 2

Ligands and Environments

5 bound ligands:
Ligand SO4 1 x SO4
Ligand GOL 3 x GOL
Ligand BME 1 x BME
Ligand URE 1 x URE
Ligand CL 1 x CL
1 modified residue:
Ligand MSE 5 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P6422
Unit cell:
a: 59.14Å b: 59.14Å c: 208.142Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.185 0.182 0.233
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.
Lee et al. (2020)
5 more

3 mentions without citation

Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods.
Gibrat et al. (2013)
2 more