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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 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' ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VP1A289Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
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Go to UniProtKB:  P04936
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VP2B261Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VP3C237Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
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Go to UniProtKB:  P04936
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VP4D68Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
LDL-receptor class A 3E39Homo sapiensMutation(s): 0 
Gene Names: VLDLR
Find proteins for P98155 (Homo sapiens)
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Go to UniProtKB:  P98155
NIH Common Fund Data Resources
PHAROS  P98155
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAO
Query on DAO

Download CCD File 
A
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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