› 4wm7

X-ray diffraction
2.32Å resolution

Crystal Structure of Human Enterovirus D68 in Complex with Pleconaril

Released:
DOI: 10.2210/pdb4wm7/pdb
PDB entry 4wm7 coloured by chain, front view.
PDB entry 4wm7 coloured by chain, side view.
PDB entry 4wm7 coloured by chain, top view.
Source organism: enterovirus D68
Primary publication:
Structure and inhibition of EV-D68, a virus that causes respiratory illness in children.
Liu Y, Sheng J, Fokine A, Meng G, Shin WH, Long F, Kuhn RJ, Kihara D, Rossmann MG
Science 347 71-4 (2015)
PMID: 25554786

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
PDBe Complex ID:
PDB-CPX-179354 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Capsid protein VP1 Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 32.78 KDa
Source organism: enterovirus D68
UniProt:
  • Canonical: Q9YLJ3 (Residues: 13-309; Coverage: 95%)
Gene name: VP1
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP2 Chain: B
Molecule details ›
Chain: B
Length: 248 amino acids
Theoretical weight: 27.71 KDa
Source organism: enterovirus D68
UniProt:
  • Canonical: Q68T42 (Residues: 70-317; Coverage: 11%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP3 Chain: C
Molecule details ›
Chain: C
Length: 247 amino acids
Theoretical weight: 27.2 KDa
Source organism: enterovirus D68
UniProt:
  • Canonical: Q68T42 (Residues: 318-564; Coverage: 11%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
VP4 Chain: D
Molecule details ›
Chain: D
Length: 68 amino acids
Theoretical weight: 7.34 KDa
Source organism: enterovirus D68
UniProt:
  • Canonical: Q8QWD4 (Residues: 2-69; Coverage: 99%)
Sequence domains: Picornavirus coat protein (VP4)

Ligands and Environments

1 bound ligand:
Ligand W11 1 x W11
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: I222
Unit cell:
a: 323.2Å b: 346.1Å c: 355.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.235 0.24

Quick links

Citations

18 review citations

The life cycle of non-polio enteroviruses and how to target it.
Baggen et al. (2018)
17 more

9 mentions without citation

Enterovirus D68 Antivirals: Past, Present, and Future.
Hu et al. (2020)
8 more