› 1k5m

X-ray diffraction
2.7Å resolution

Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2

Released:
DOI: 10.2210/pdb1k5m/pdb
PDB entry 1k5m coloured by chain, front view.
PDB entry 1k5m coloured by chain, side view.
PDB entry 1k5m coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of a human rhinovirus that displays part of the HIV-1 V3 loop and induces neutralizing antibodies against HIV-1.
Ding J, Smith AD, Geisler SC, Ma X, Arnold GF, Arnold E
Structure 10 999-1011 (2002)
PMID: 12121655

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 domain:

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136734 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Capsid protein VP1 Chain: A
Molecule details ›
Chain: A
Length: 289 amino acids
Theoretical weight: 32.56 KDa
Source organism: rhinovirus B14
Expression system: Homo sapiens
UniProt:
  • Canonical: P03303 (Residues: 568-856; Coverage: 13%)
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP2; Surface protein gp120 Chain: B
Molecule details ›
Chain: B
Length: 277 amino acids
Theoretical weight: 30.1 KDa
Source organisms: Expression system: Homo sapiens
UniProt:
  • Canonical: P03303 (Residues: 70-228, 229-331; Coverage: 12%)
  • Canonical: P05877 (Residues: 314-325; Coverage: 2%)
Gene name: env
Sequence domains: picornavirus capsid protein
Structure domains: Jelly Rolls
Capsid protein VP3 Chain: C
Molecule details ›
Chain: C
Length: 236 amino acids
Theoretical weight: 26.24 KDa
Source organism: rhinovirus B14
Expression system: Homo sapiens
UniProt:
  • Canonical: P03303 (Residues: 332-567; 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: 7.18 KDa
Source organism: rhinovirus B14
Expression system: Homo sapiens
UniProt:
  • Canonical: P03303 (Residues: 2-69; Coverage: 3%)
Sequence domains: Picornavirus coat protein (VP4)
Structure domains: Picornavirus coat protein VP4

Ligands and Environments

1 bound ligand:
Ligand SPH 1 x SPH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25, CHESS BEAMLINE F1
Spacegroup: I222
Unit cell:
a: 318.9Å b: 349.3Å c: 368.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 not available
Expression system: Homo sapiens

Quick links

Citations

1 review citation

V3: HIV's switch-hitter.
Hartley et al. (2005)
19 other articles

3 mentions without citation

Molecular analysis of virulent determinants of enterovirus 71.
Li et al. (2011)
2 more