1V9U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.285 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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.

(2004) Nat Struct Mol Biol 11: 429-434

  • DOI: https://doi.org/10.1038/nsmb753
  • Primary Citation of Related Structures:  
    1V9U

  • PubMed Abstract: 

    Although many viral receptors have been identified, the ways in which they interact with their cognate viruses are not understood at the molecular level. We have determined the X-ray structure of a complex between calcium-containing modules of the very low-density lipoprotein receptor and the minor group human rhinovirus HRV2. The receptor binds close to the icosahedral five-fold vertex, with only one module per virus protomer. The binding face of this module is defined by acidic calcium-chelating residues and, in particular, by an exposed tryptophan that is highly conserved. The attachment site on the virus involves only residues from VP1, particularly a lysine strictly conserved in all minor group HRVs. The disposition of the attached ligand-binding repeats around the five-fold axis, together with the proximity of the N- and C-terminal ends of adjacent modules, suggests that more than one repeat in a single receptor molecule might attach simultaneously.


  • Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi Girona 18-26, E-08034 Barcelona, Spain. nvmcri@ibmb.csis.es


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coat protein VP1A [auth 1]289rhinovirus A2Mutation(s): 0 
UniProt
Find proteins for P04936 (Human rhinovirus 2)
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Go to UniProtKB:  P04936
Entity Groups  
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UniProt GroupP04936
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coat protein VP2B [auth 2]261rhinovirus A2Mutation(s): 0 
UniProt
Find proteins for P04936 (Human rhinovirus 2)
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Go to UniProtKB:  P04936
Entity Groups  
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UniProt GroupP04936
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Coat protein VP3C [auth 3]237rhinovirus A2Mutation(s): 0 
UniProt
Find proteins for P04936 (Human rhinovirus 2)
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Go to UniProtKB:  P04936
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UniProt GroupP04936
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Coat protein VP4D [auth 4]68rhinovirus A2Mutation(s): 0 
UniProt
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
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UniProt GroupP04936
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
LDL-receptor class A 3E [auth 5]41Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P98155 (Homo sapiens)
Explore P98155 
Go to UniProtKB:  P98155
PHAROS:  P98155
GTEx:  ENSG00000147852 
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UniProt GroupP98155
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DAO
Query on DAO

Download Ideal Coordinates CCD File 
F [auth 1]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth 5]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.285 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 313.1α = 90
b = 348.79β = 90
c = 380.89γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description