3DPR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.441 
  • R-Value Work: 0.425 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein VP1
A
289Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein VP2
B
261Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein VP3
C
237Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Protein VP4
D
68Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
LDL-receptor class A 3
E
39Homo sapiensMutation(s): 0 
Gene Names: VLDLR
Find proteins for P98155 (Homo sapiens)
Go to Gene View: VLDLR
Go to UniProtKB:  P98155
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DAO
Query on DAO

Download SDF File 
Download CCD File 
A
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.441 
  • R-Value Work: 0.425 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 498.117α = 90.00
b = 498.117β = 90.00
c = 658.425γ = 90.00
Software Package:
Software NamePurpose
DMphasing
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
ADSCdata collection
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-01-30
    Type: Refinement description
  • Version 1.3: 2017-10-25
    Type: Advisory, Refinement description