1FPN

HUMAN RHINOVIRUS SEROTYPE 2 (HRV2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of human rhinovirus serotype 2 (HRV2).

Verdaguer, N.Blaas, D.Fita, I.

(2000) J.Mol.Biol. 300: 1179-1194

  • DOI: 10.1006/jmbi.2000.3943

  • PubMed Abstract: 
  • Human rhinoviruses are classified into a major and a minor group based on their binding to ICAM-1 or to members of the LDL-receptor family, respectively. They can also be divided into groups A and B, according to their sensitivity towards a panel of ...

    Human rhinoviruses are classified into a major and a minor group based on their binding to ICAM-1 or to members of the LDL-receptor family, respectively. They can also be divided into groups A and B, according to their sensitivity towards a panel of antiviral compounds. The structure of human rhinovirus 2 (HRV2), which uses the LDL receptor for cell attachment and is included in antiviral group B, has been solved and refined at 2.6 A resolution by X-ray crystallography to gain information on the peculiarities of rhinoviruses, in particular from the minor receptor group. The main structural differences between HRV2 and other rhinoviruses, including the minor receptor group serotype HRV1A, are located at the internal protein shell surface and at the external antigenic sites. In the interior, the N termini of VP1 and VP4 form a three-stranded beta-sheet in an arrangement similar to that present in poliovirus, although myristate was not visible at the amino terminus of VP4 in the HRV2 structure. The betaE-betaF loop of VP2, a linear epitope within antigenic site B recognized by monoclonal antibody 8F5, adopts a conformation considerably different from that found in the complex of 8F5 with a synthetic peptide of the same sequence. This either points to considerable structural changes impinged on this loop upon antibody binding, or to the existence of more than one single conformation of the loop when the virus is in solution. The hydrophobic pocket of VP1 was found to be occupied by a pocket factor apparently identical with that present in the major receptor group virus HRV16. Electron density, consistent with the presence of a viral RNA fragment, is seen stacked against a conserved tryptophan residue.


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona (CSIC), Jordi Girona 18-26, Barcelona, 08034, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN VP1
1
289Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN VP2
2
261Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN VP3
3
237Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN VP4
4
68Human rhinovirus 2Mutation(s): 0 
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAO
Query on DAO

Download SDF File 
Download CCD File 
1
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 308.680α = 90.00
b = 352.980β = 90.00
c = 380.480γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
X-PLORmodel building
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance