2R07

STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.

Badger, J.Minor, I.Oliveira, M.A.Smith, T.J.Rossmann, M.G.

(1989) Proteins 6: 1-19

  • DOI: 10.1002/prot.340060102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electr ...

    X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.


    Related Citations: 
    • Three-Dimensional Structures of Drug-Resistant Mutants of Human Rhinovirus 14
      Badger, J.,Krishnaswamy, S.,Kremer, M.J.,Oliveira, M.A.,Rossmann, M.G.,Heinz, B.A.,Rueckert, R.R.,Dutko, F.J.,Mckinlay, M.A.
      (1989) J.Mol.Biol. 207: 163
    • Implications of the Picornavirus Capsid Structure for Polyprotein Structure
      Arnold, E.,Luo, M.,Vriend, G.,Rossmann, M.G.,Palmenberg, A.C.,Parks, G.D.,Nicklin, M.J.H.,Wimmer, E.
      (1987) Proc.Natl.Acad.Sci.USA 84: 21
    • The Structure of a Human Common Cold Virus (Rhinovirus 14) and its Evolutionary Relations to Other Viruses
      Rossmann, M.G.,Arnold, E.,Erickson, J.W.,Frankenberger, E.A.,Griffith, J.P.,Hecht, H.-J.,Johnson, J.E.,Kamer, G.,Luo, M.,Vriend, G.
      (1987) Chem.Scr. 26: 313
    • The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
      Smith, T.J.,Kremer, M.J.,Luo, M.,Vriend, G.,Arnold, E.,Kamer, G.,Rossmann, M.G.,Mckinlay, M.A.,Diana, G.D.,Otto, M.J.
      (1986) Science 233: 1286
    • Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
      Rossmann, M.G.,Arnold, E.,Erickson, J.W.,Frankenberger, E.A.,Griffith, J.P.,Hecht, H.-J.,Johnson, J.E.,Kamer, G.,Luo, M.,Mosser, A.G.,Rueckert, R.R.,Sherry, B.,Vriend, G.
      (1985) Nature 317: 145
    • Picornaviruses of Two Different Genera Have Similar Structures
      Luo, M.,Arnold, E.,Erickson, J.W.,Rossmann, M.G.,Boege, U.,Scraba, D.G.
      (1984) J.Mol.Biol. 180: 703
    • Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 Angstroms
      Arnold, E.,Rossmann, M.G.
      () TO BE PUBLISHED --: --
    • The Use of Molecular Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure
      Arnold, E.,Rossmann, M.G.
      () TO BE PUBLISHED --: --
    • Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14
      Badger, J.,Minor, I.,Kremer, M.J.,Oliveira, M.A.,Smith, T.J.,Griffith, J.P.,Guerin, D.M.A.,Krishnaswamy, S.,Luo, M.,Rossmann, M.G.,Mckinlay, M.A.,Diana, G.D.,Dutko, F.J.,Fancher, M.,Rueckert, R.R.,Heinz, B.A.
      (1988) Proc.Natl.Acad.Sci.USA 85: 3304
    • Crystallization of a Common Cold Virus, Human Rhinovirus 14. (Quote)Isomorphism(Quote) with Poliovirus Crystals
      Erickson, J.W.,Frankenberger, E.A.,Rossmann, M.G.,Fout, G.S.,Medappa, K.C.,Rueckert, R.R.
      (1983) Proc.Natl.Acad.Sci.USA 80: 931
    • The Structure Determination of a Common Cold Virus, Human Rhinovirus 14
      Arnold, E.,Vriend, G.,Luo, M.,Griffith, J.P.,Kamer, G.,Erickson, J.W.,Johnson, J.E.,Rossmann, M.G.
      (1987) Acta Crystallogr.,Sect.A 43: 346
    • Virion Orientation in Cubic Crystals of the Human Common Cold Virus Hrv14
      Arnold, E.,Erickson, J.W.,Fout, G.S.,Frankenberger, E.A.,Hecht, H.-J.,Luo, M.,Rossmann, M.G.,Rueckert, R.R.
      (1984) J.Mol.Biol. 177: 417


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)
1
289Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)
2
262Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)
3
236Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)
4
68Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
W33
Query on W33

Download SDF File 
Download CCD File 
1
5-(5-(6-CHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-METHYL ISOXAZOLE
COMPOUND VII
C18 H21 Cl N2 O3
FCSKOFQQCWLGMV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 445.100α = 90.00
b = 445.100β = 90.00
c = 445.100γ = 90.00
Software Package:
Software NamePurpose
REAL-SPACErefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-01-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance