3DPR image
Deposition Date 2008-07-09
Release Date 2009-04-07
Last Version Date 2024-10-30
Entry Detail
PDB ID:
3DPR
Keywords:
VIRUS
Title:
Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Human rhinovirus 2 (Taxon ID: 12130)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.50 Å
R-Value Free:
0.44
R-Value Work:
0.42
R-Value Observed:
0.42
Space Group:
P 43 21 2
3DPR validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein VP1
Chain IDs:A
Chain Length:289
Number of Molecules:1
Biological Source:Human rhinovirus 2
UniProt ID:P04936 Pfam ID:PF00073, PF02226
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein VP2
Chain IDs:B
Chain Length:261
Number of Molecules:1
Biological Source:Human rhinovirus 2
UniProt ID:P04936 Pfam ID:PF00073, PF02226
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein VP3
Chain IDs:C
Chain Length:237
Number of Molecules:1
Biological Source:Human rhinovirus 2
UniProt ID:P04936 Pfam ID:PF00073, PF02226
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein VP4
Chain IDs:D
Chain Length:68
Number of Molecules:1
Biological Source:Human rhinovirus 2
UniProt ID:P04936 Pfam ID:PF00073, PF02226
Protein Blast
Polymer Type:polypeptide(L)
Molecule:LDL-receptor class A 3
Gene (Uniprot):VLDLR
Chain IDs:E
Chain Length:39
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P98155 Pfam ID:PF00057
Ligand Molecules
CA
DAO
Primary Citation
Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition
Febs Lett. 583 235 240 (2009)
PMID: 19073182 DOI: 10.1016/j.febslet.2008.12.014

Abstact

X-ray structures of human rhinovirus 2 (HRV2) in complex with soluble very-low-density lipoprotein receptors encompassing modules 1, 2, and 3 (V123) and five V3 modules arranged in tandem (V33333) demonstrates multi-modular binding around the virion's five-fold axes. Occupancy was 60% for V123 and 100% for V33333 explaining the high-avidity of the interaction. Surface potentials of 3D-models of all minor group HRVs and K-type major group HRVs were compared; hydrophobic interactions between a conserved lysine in the viruses and a tryptophan in the receptor modules together with coulombic attraction via diffuse opposite surface potentials determine minor group HRV receptor specificity.

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Primary Citation of related structures
3DPR