› 4dw4

X-ray diffraction
2.23Å resolution

Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with 5'-UMP

Released:
DOI: 10.2210/pdb4dw4/pdb
PDB entry 4dw4 coloured by chain, front view.
PDB entry 4dw4 coloured by chain, side view.
PDB entry 4dw4 coloured by chain, top view.
Source organism: Bovine viral diarrhea virus 1-CP7
Primary publication:
Crystal structure of the pestivirus envelope glycoprotein E(rns) and mechanistic analysis of its ribonuclease activity.
Krey T, Bontems F, Vonrhein C, Vaney MC, Bricogne G, Rümenapf T, Rey FA
Structure 20 862-73 (2012)
PMID: 22579253

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Leu is conserved at position P1 for all four cleavage sites. Alanine is found at position P1' of the NS4A-NS4B cleavage site, whereas serine is found at position P1' of the NS3-NS4A, NS4B-NS5A and NS5A-NS5B cleavage sites
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
(1a) RNA = an (RNA fragment)-3'-nucleoside-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-(RNA fragment)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188318 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
E(rns) glycoprotein Chains: A, B
Molecule details ›
Chains: A, B
Length: 167 amino acids
Theoretical weight: 19.01 KDa
Source organism: Bovine viral diarrhea virus 1-CP7
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q96662 (Residues: 271-435; Coverage: 4%)
Structure domains: Ribonuclease T2-like

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand NAG 3 x NAG
Ligand SO4 3 x SO4
Ligand U5P 4 x U5P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21212
Unit cell:
a: 72.35Å b: 107.97Å c: 64.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.207 0.246
Expression system: Drosophila melanogaster

Quick links

Citations

7 review citations

Immune Responses Against Classical Swine Fever Virus: Between Ignorance and Lunacy.
Summerfield et al. (2015)
6 more

1 mention without citation

Protein signatures using electrostatic molecular surfaces in harmonic space.
Carvalho et al. (2013)