› 3bsn

X-ray diffraction
1.8Å resolution

Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA

Released:
DOI: 10.2210/pdb3bsn/pdb
PDB entry 3bsn coloured by chain, front view.
PDB entry 3bsn coloured by chain, side view.
PDB entry 3bsn coloured by chain, top view.
Source organism: Norwalk virus
Primary publication:
Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase.
Zamyatkin DF, Parra F, Alonso JM, Harki DA, Peterson BR, Grochulski P, Ng KK
J Biol Chem 283 7705-12 (2008)
PMID: 18184655

Function and Biology Details

Reaction catalysed: 
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180674 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
RNA dependent RNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 510 amino acids
Theoretical weight: 56.84 KDa
Source organism: Norwalk virus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q70ET3 (Residues: 329-838; Coverage: 61%)
Sequence domains: Viral RNA-dependent RNA polymerase
Structure domains:
RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3') Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.56 KDa
Source organism: Norwalk virus
Expression system: Not provided
RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*GP*(N5M))-3') Chain: T
Molecule details ›
Chain: T
Length: 9 nucleotides
Theoretical weight: 2.91 KDa
Source organism: Norwalk virus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand GOL 4 x GOL
Ligand MN 3 x MN
Ligand N5C 1 x N5C
1 modified residue:
Ligand N5M 1 x N5M

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 74.31Å b: 93.85Å c: 96.03Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.201 0.236
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

18 review citations

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution.
Venkataraman et al. (2018)
17 more

7 mentions without citation

Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses.
Deval et al. (2017)
6 more