› 5y3d

X-ray diffraction
3.14Å resolution

Structural insight into the interaction between RNA polymerase and VPg for norovirus replication

Released:
DOI: 10.2210/pdb5y3d/pdb
PDB entry 5y3d coloured by chain, front view.
PDB entry 5y3d coloured by chain, side view.
PDB entry 5y3d coloured by chain, top view.
Source organisms:
Primary publication:
Insight Into the Interaction Between RNA Polymerase and VPg for Murine Norovirus Replication.
Lee JH, Park BS, Han KR, Biering SB, Kim SJ, Choi J, Seok JH, Alam I, Chung MS, Kim HM, Hwang S, Kim KH
Front Microbiol 9 1466 (2018)
PMID: 30038601

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166328 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
RNA-directed RNA polymerase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 517 amino acids
Theoretical weight: 58.52 KDa
Source organism: Murine norovirus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q80J95 (Residues: 1181-1686; Coverage: 30%)
Gene name: ORF1
Sequence domains: Viral RNA-dependent RNA polymerase
Structure domains:
viral protein genome-linked (VPg) Chains: G, H
Molecule details ›
Chains: G, H
Length: 35 amino acids
Theoretical weight: 3 KDa
Source organism: Murine norovirus
Expression system: Escherichia coli

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21
Unit cell:
a: 109.172Å b: 159.729Å c: 121.704Å
α: 90° β: 97.24° γ: 90°
R-values:
R R work R free
0.204 0.202 0.241
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Calicivirus RNA-Dependent RNA Polymerases: Evolution, Structure, Protein Dynamics, and Function.
Smertina et al. (2019)
2 more

2 mentions without citation

Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies.
Ramaswamy et al. (2022)
1 more