› 5bnp

X-ray diffraction
2.15Å resolution

Crystal structure of human enterovirus D68 in complex with 3'SLN

Released:
DOI: 10.2210/pdb5bnp/pdb
PDB entry 5bnp coloured by chain, front view.
PDB entry 5bnp coloured by chain, side view.
PDB entry 5bnp coloured by chain, top view.
Source organism: enterovirus D68
Primary publication:
Sialic acid-dependent cell entry of human enterovirus D68.
Liu Y, Sheng J, Baggen J, Meng G, Xiao C, Thibaut HJ, van Kuppeveld FJ, Rossmann MG
Nat Commun 6 8865 (2015)
PMID: 26563423

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:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179353 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 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: Q68T42 (Residues: 565-861; Coverage: 14%)
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
Capsid protein VP4 Chain: D
Molecule details ›
Chain: D
Length: 68 amino acids
Theoretical weight: 7.34 KDa
Source organism: enterovirus D68
UniProt:
  • Canonical: Q68T42 (Residues: 2-69; Coverage: 3%)
Sequence domains: Picornavirus coat protein (VP4)

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, GAL, SIA
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: I222
Unit cell:
a: 325.8Å b: 347.2Å c: 356.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.244 0.244 0.246

Quick links

Citations

23 review citations

Enterovirus D68 and acute flaccid myelitis-evaluating the evidence for causality.
Messacar et al. (2018)
22 more

2 mentions without citation

Sialic acid-dependent cell entry of human enterovirus D68.
Liu et al. (2015)
1 more