› 5zit

X-ray diffraction
3.2Å resolution

Crystal structure of human Enterovirus D68 RdRp in complex with NADPH

Released:
DOI: 10.2210/pdb5zit/pdb
PDB entry 5zit coloured by chain, front view.
PDB entry 5zit coloured by chain, side view.
PDB entry 5zit coloured by chain, top view.
Source organism: enterovirus D68
Primary publication:
Structure of the enterovirus D68 RNA-dependent RNA polymerase in complex with NADPH implicates an inhibitor binding site in the RNA template tunnel.
Li L, Wang M, Chen Y, Hu T, Yang Y, Zhang Y, Bi G, Wang W, Liu E, Han J, Lu T, Su D
J Struct Biol 211 107510 (2020)
PMID: 32353513

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125154 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RdRp Chain: A
Molecule details ›
Chain: A
Length: 457 amino acids
Theoretical weight: 51.91 KDa
Source organism: enterovirus D68
Expression system: Escherichia coli
UniProt:
  • Canonical: I6TFG7 (Residues: 1731-2187; Coverage: 21%)
Sequence domains: Viral RNA-dependent RNA polymerase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand NDP 1 x NDP
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P41212
Unit cell:
a: 60.683Å b: 60.683Å c: 360.518Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.251 0.248 0.314
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Identification of Mulberrofuran as a potent inhibitor of hepatitis A virus 3Cpro and RdRP enzymes through structure-based virtual screening, dynamics simulation, and DFT studies.
Sureshan et al. (2023)

2 mentions without citation

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