3DPR

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.441 
  • R-Value Work: 0.425 
  • R-Value Observed: 0.426 

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This is version 1.4 of the entry. See complete history. 


Literature

Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition

Querol-Audi, J., Konecsni, T., Pous, J., Carugo, O., Fita, I., Verdaguer, N., Blaas, D.

(2009) FEBS Lett 583: 235-240

  • DOI: https://doi.org/10.1016/j.febslet.2008.12.014
  • Primary Citation of Related Structures:  
    3DPR

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 

    Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VP1289rhinovirus A2Mutation(s): 0 
UniProt
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04936
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VP2261rhinovirus A2Mutation(s): 0 
UniProt
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04936
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VP3237rhinovirus A2Mutation(s): 0 
UniProt
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04936
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein VP468rhinovirus A2Mutation(s): 0 
UniProt
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
Entity Groups  
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UniProt GroupP04936
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
LDL-receptor class A 339Homo 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 
Entity Groups  
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UniProt GroupP98155
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DAO
Query on DAO
Download Ideal Coordinates CCD File 
F [auth A]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
G [auth E]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.441 
  • R-Value Work: 0.425 
  • R-Value Observed: 0.426 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 498.117α = 90
b = 498.117β = 90
c = 658.425γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-01-30
    Changes: Refinement description
  • Version 1.3: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary