› 3dpr

X-ray diffraction
3.5Å resolution

Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3

Released:
DOI: 10.2210/pdb3dpr/pdb
PDB entry 3dpr coloured by chain, front view.
PDB entry 3dpr coloured by chain, side view.
PDB entry 3dpr coloured by chain, top view.
Source organisms:
Primary publication:
Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition.
Querol-Audí J, Konecsni T, Pous J, Carugo O, Fita I, Verdaguer N, Blaas D
FEBS Lett 583 235-40 (2009)
PMID: 19073182

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 300-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138285 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Capsid protein VP1 Chain: A
Molecule details ›
Chain: A
Length: 289 amino acids
Theoretical weight: 32.92 KDa
Source organism: rhinovirus A2
UniProt:
  • Canonical: P04936 (Residues: 568-856; Coverage: 13%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP2 Chain: B
Molecule details ›
Chain: B
Length: 261 amino acids
Theoretical weight: 29.01 KDa
Source organism: rhinovirus A2
UniProt:
  • Canonical: P04936 (Residues: 70-330; Coverage: 12%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP3 Chain: C
Molecule details ›
Chain: C
Length: 237 amino acids
Theoretical weight: 26.11 KDa
Source organism: rhinovirus A2
UniProt:
  • Canonical: P04936 (Residues: 331-567; 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: 7.36 KDa
Source organism: rhinovirus A2
UniProt:
  • Canonical: P04936 (Residues: 2-69; Coverage: 3%)
Sequence domains: Picornavirus coat protein (VP4)
Very low-density lipoprotein receptor Chain: E
Molecule details ›
Chain: E
Length: 39 amino acids
Theoretical weight: 4.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P98155 (Residues: 113-151; Coverage: 5%)
Gene name: VLDLR
Sequence domains: Low-density lipoprotein receptor domain class A

Ligands and Environments

2 bound ligands:
Ligand DAO 1 x DAO
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P43212
Unit cell:
a: 498.117Å b: 498.117Å c: 658.425Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.426 0.425 0.441
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Uncoating of human rhinoviruses.
Fuchs et al. (2010)
1 more

6 mentions without citation

3D Recognition Based on Sensor Modalities for Robotic Systems: A Survey.
Manzoor et al. (2021)
5 more