1R08

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 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:  
    1R08, 2R04, 2R06, 2R07, 2RM2, 2RR1, 2RS1, 2RS3, 2RS5

  • 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 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 ...

    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: 
    • The Use of Molecular Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure
      Arnold, E., Rossmann, M.G.
      () To be published --: --
    • 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 --: --
    • 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
    • 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 U S A 85: 3304
    • 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 A 43: 346
    • 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 U S A 84: 21
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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 U S A 80: 931
    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)A [auth 1]289rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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Entity Groups  
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UniProt GroupP03303
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)B [auth 2]262rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)C [auth 3]236rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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UniProt GroupP03303
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)D [auth 4]68rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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Go to UniProtKB:  P03303
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UniProt GroupP03303
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
W42
Query on W42
Download Ideal Coordinates CCD File 
E [auth 1]5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYL OXYMETHYLENEOXYMETHYL) ISOXAZOLE
C21 H26 Cl2 N2 O6
JLSNWEWWUSOSMP-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 445.1α = 90
b = 445.1β = 90
c = 445.1γ = 90
Software Package:
Software NamePurpose
REAL-SPACErefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1990-01-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance