› 1v9u

X-ray diffraction
3.6Å resolution

Human Rhinovirus 2 bound to a fragment of its cellular receptor protein

Released:
DOI: 10.2210/pdb1v9u/pdb
PDB entry 1v9u coloured by chain, front view.
PDB entry 1v9u coloured by chain, side view.
PDB entry 1v9u coloured by chain, top view.
Source organisms:
Primary publication:
X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein.
Verdaguer N, Fita I, Reithmayer M, Moser R, Blaas D
Nat Struct Mol Biol 11 429-34 (2004)
PMID: 15064754

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 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: 1
Molecule details ›
Chain: 1
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: 2
Molecule details ›
Chain: 2
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: 3
Molecule details ›
Chain: 3
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: 4
Molecule details ›
Chain: 4
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: 5
Molecule details ›
Chain: 5
Length: 41 amino acids
Theoretical weight: 4.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P98155 (Residues: 111-151; 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 ID14-4
Unit cell:
a: 313.1Å b: 348.79Å c: 380.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.285 0.285 0.295
Expression system: Escherichia coli

Quick links

Citations

16 review citations

Structure and physiologic function of the low-density lipoprotein receptor.
Jeon et al. (2005)
15 more

3 mentions without citation

Versatility in ligand recognition by LDL receptor family proteins: advances and frontiers.
Blacklow SC. (2007)
2 more