1AYM

HUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle.

Hadfield, A.T.Lee, W.Zhao, R.Oliveira, M.A.Minor, I.Rueckert, R.R.Rossmann, M.G.

(1997) Structure 5: 427-441

  • DOI: 10.1016/s0969-2126(97)00199-8
  • Primary Citation of Related Structures:  
    1AYM

  • PubMed Abstract: 
  • Rhinoviruses belong to the picornavirus family and are small, icosahedral, non-enveloped viruses containing one positive RNA strand. Human rhinovirus 16 (HRV16) belongs to the major receptor group of rhinoviruses, for which the cellular receptor is inter ...

    Rhinoviruses belong to the picornavirus family and are small, icosahedral, non-enveloped viruses containing one positive RNA strand. Human rhinovirus 16 (HRV16) belongs to the major receptor group of rhinoviruses, for which the cellular receptor is intercellular adhesion molecule-1 (ICAM-1). In many rhinoviruses, one of the viral coat proteins (VP1) contains a hydrophobic pocket which is occupied by a fatty acid-like molecule, or so-called 'pocket factor'. Antiviral agents have been shown to bind to the hydrophobic pocket in VP1, replacing the pocket factor. The presence of the antiviral compound blocks uncoating of the virus and in some cases inhibits receptor attachment. A refined, high-resolution structure would be expected to provide further information on the nature of the pocket factor and other features previously not clearly identified.


    Related Citations: 
    • The Structure of Human Rhinovirus 16
      Oliveira, M.A., Zhao, R., Lee, W.M., Kremer, M.J., Minor, I., Rueckert, R.R., Diana, G.D., Pevear, D.C., Dutko, F.J., Mckinlay, M.A., Rossmann, M.G.
      (1993) Structure 1: 51
    • A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A
      Kim, K.H., Willingmann, P., Gong, Z.X., Kremer, M.J., Chapman, M.S., Minor, I., Oliveira, M.A., Rossmann, M.G., Andries, K., Diana, G.D., Dutko, F.J., Mckinlay, M.A., Pevear, D.C.
      (1993) J Mol Biol 230: 206
    • Structure of a Human Rhinovirus Complexed with its Receptor Molecule
      Olson, N.H., Kolatkar, P.R., Oliveira, M.A., Cheng, R.H., Greve, J.M., Mcclelland, A., Baker, T.S., Rossmann, M.G.
      (1993) Proc Natl Acad Sci U S A 90: 507
    • Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
      Kim, S.S., Smith, T.J., Chapman, M.S., Rossmann, M.G., Pevear, D.C., Dutko, F.J., Felock, P.J., Diana, G.D., Mckinlay, M.A.
      (1989) J Mol Biol 210: 91
    • Common Cold Viruses
      Rossmann, M.G., Arnold, E., Griffith, J.P., Kamer, G., Luo, M., Smith, T.J., Vriend, G., Rueckert, R.R., Sherry, B., Mckinlay, M.A., Diana, G., Otto, M.
      (1987) Trends Biochem Sci 12: 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

    Organizational Affiliation

    Department of Biological Sciences, Purdue University West Lafayette, IN 47907-1392, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 16 COAT PROTEIN 1285Human rhinovirus sp.Mutation(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 Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 16 COAT PROTEIN 2261Human rhinovirus sp.Mutation(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 Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 16 COAT PROTEIN 3238Human rhinovirus sp.Mutation(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 Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 16 COAT PROTEIN 468Human rhinovirus sp.Mutation(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 P23008 (Human rhinovirus 1A)
Explore P23008 
Go to UniProtKB:  P23008
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download Ideal Coordinates CCD File 
4
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
DAO
Query on DAO

Download Ideal Coordinates CCD File 
1
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
1
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 362.6α = 90
b = 347.1β = 90
c = 334.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-07-04
    Changes: Advisory, Data collection, Derived calculations, Other