› 5mjv

X-ray diffraction
3.09Å resolution

Rebuild and re-refined model for Human Parechovirus 1

Released:
DOI: 10.2210/pdb5mjv/pdb
PDB entry 5mjv coloured by chain, front view.
PDB entry 5mjv coloured by chain, side view.
PDB entry 5mjv coloured by chain, top view.
Source organism: Echovirus 22 (strain Harris)
Primary publication:
Genomic RNA folding mediates assembly of human parechovirus.
Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJB, Butcher SJ, Stockley PG, Twarock R
Nat Commun 8 5 (2017)
PMID: 28232749

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.
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179256 (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
Capsid protein VP1 Chain: A
Molecule details ›
Chain: A
Length: 234 amino acids
Theoretical weight: 26.42 KDa
Source organism: Echovirus 22 (strain Harris)
Expression system: Homo sapiens
UniProt:
  • Canonical: Q66578 (Residues: 543-776; Coverage: 11%)
Capsid protein VP3 Chain: B
Molecule details ›
Chain: B
Length: 253 amino acids
Theoretical weight: 28.29 KDa
Source organism: Echovirus 22 (strain Harris)
Expression system: Homo sapiens
UniProt:
  • Canonical: Q66578 (Residues: 290-542; Coverage: 12%)
Structure domains: Jelly Rolls
Capsid protein VP0 Chain: C
Molecule details ›
Chain: C
Length: 289 amino acids
Theoretical weight: 31.69 KDa
Source organism: Echovirus 22 (strain Harris)
Expression system: Homo sapiens
UniProt:
  • Canonical: Q66578 (Residues: 1-289; Coverage: 13%)
Sequence domains: picornavirus capsid protein
RNA (5'-R(*GP*UP*UP*UP*UP*U)-3') Chain: D
Molecule details ›
Chain: D
Length: 6 nucleotides
Theoretical weight: 1.83 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P6322
Unit cell:
a: 399.5Å b: 399.5Å c: 332.86Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.258 0.258 0.261
Expression system: Homo sapiens

Quick links

Citations

9 review citations

Cryo-electron microscopy for the study of virus assembly.
Luque et al. (2020)
8 more

4 mentions without citation

Genomic RNA folding mediates assembly of human parechovirus.
Shakeel et al. (2017)
3 more