› 1s49

X-ray diffraction
3Å resolution

Crystal Structure of RNA-dependent RNA polymerase construct 1 (residues 71-679) from bovine viral diarrhea virus complexed with GTP

Released:
DOI: 10.2210/pdb1s49/pdb
PDB entry 1s49 coloured by chain, front view.
PDB entry 1s49 coloured by chain, side view.
PDB entry 1s49 coloured by chain, top view.
Source organism: Bovine viral diarrhea virus 1
Primary publication:
The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation.
Choi KH, Groarke JM, Young DC, Kuhn RJ, Smith JL, Pevear DC, Rossmann MG
Proc Natl Acad Sci U S A 101 4425-30 (2004)
PMID: 15070734

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:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-148695 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA-directed RNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 609 amino acids
Theoretical weight: 70.49 KDa
Source organism: Bovine viral diarrhea virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P19711 (Residues: 3340-3948; Coverage: 15%)
Sequence domains: Viral RNA dependent RNA polymerase
Structure domains: Alpha-Beta Plaits

Ligands and Environments

1 bound ligand:
Ligand GTP 1 x GTP
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P6222
Unit cell:
a: 205.727Å b: 205.727Å c: 99.597Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.268 0.264 0.266
Expression system: Escherichia coli

Quick links

Citations

25 review citations

Structure and functionality in flavivirus NS-proteins: perspectives for drug design.
Bollati et al. (2010)
24 more

10 mentions without citation

RNA synthetic mechanisms employed by diverse families of RNA viruses.
McDonald SM. (2013)
9 more