› 4qpx

X-ray diffraction
1.86Å resolution

NV polymerase post-incorporation-like complex

Released:
DOI: 10.2210/pdb4qpx/pdb
PDB entry 4qpx coloured by chain, front view.
PDB entry 4qpx coloured by chain, side view.
PDB entry 4qpx coloured by chain, top view.
Source organism: Norwalk virus
Primary publication:
Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase.
Zamyatkin D, Rao C, Hoffarth E, Jurca G, Rho H, Parra F, Grochulski P, Ng KK
Acta Crystallogr D Biol Crystallogr 70 3099-109 (2014)
PMID: 25478829

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-180678 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Polyprotein 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: 331-838; 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(*U*AP*CP*CP*CP*GP*GP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 8 nucleotides
Theoretical weight: 2.54 KDa
Source organism: Norwalk virus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand GOL 2 x GOL
Ligand MN 3 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P41212
Unit cell:
a: 81.22Å b: 81.22Å c: 188.13Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.205 0.253
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

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

4 mentions without citation

Emergence of norovirus strains: A tale of two genes.
Parra GI. (2019)
3 more