› 3vbf

X-ray diffraction
2.6Å resolution

Crystal structure of formaldehyde treated human Enterovirus 71 (space group I23)

Released:
DOI: 10.2210/pdb3vbf/pdb
PDB entry 3vbf coloured by chain, front view.
PDB entry 3vbf coloured by chain, side view.
PDB entry 3vbf coloured by chain, top view.
Source organism: Enterovirus A71
Primary publication:
A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.
Wang X, Peng W, Ren J, Hu Z, Xu J, Lou Z, Li X, Yin W, Shen X, Porta C, Walter TS, Evans G, Axford D, Owen R, Rowlands DJ, Wang J, Stuart DI, Fry EE, Rao Z
OpenAccess logo Nat Struct Mol Biol 19 424-9 (2012)
PMID: 22388738

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-109785 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Genome Polyprotein, capsid protein VP1 Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 32.73 KDa
Source organism: Enterovirus A71
UniProt:
  • Canonical: B2ZUN0 (Residues: 566-862; Coverage: 14%)
Sequence domains: Picornavirus coat protein
Structure domains: Jelly Rolls
Genome Polyprotein, capsid protein VP2 Chain: B
Molecule details ›
Chain: B
Length: 245 amino acids
Theoretical weight: 26.87 KDa
Source organism: Enterovirus A71
UniProt:
  • Canonical: B2ZUN0 (Residues: 79-323; Coverage: 11%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Genome Polyprotein, capsid protein VP3 Chain: C
Molecule details ›
Chain: C
Length: 242 amino acids
Theoretical weight: 26.47 KDa
Source organism: Enterovirus A71
UniProt:
  • Canonical: B2ZUN0 (Residues: 324-565; Coverage: 11%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Genome Polyprotein, capsid protein VP4 Chain: D
Molecule details ›
Chain: D
Length: 58 amino acids
Theoretical weight: 6.38 KDa
Source organism: Enterovirus A71
UniProt:
  • Canonical: B2ZUN0 (Residues: 12-69; Coverage: 3%)
Sequence domains: Picornavirus coat protein (VP4)
Structure domains: Rhinovirus 14, subunit 4

Ligands and Environments

5 bound ligands:
Ligand SPH 1 x SPH
Ligand AMP 1 x AMP
Ligand K 2 x K
Ligand NA 1 x NA
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: I23
Unit cell:
a: 600.1Å b: 600.1Å c: 600.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.236 0.24

Quick links

Citations

27 review citations

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

16 mentions without citation

A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.
Wang et al. (2012)
15 more