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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Also Cited By: 1QJU, 1QJX, 1QJY

  • 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 i ...

    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 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 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.USA 90: 507
    • 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
    • 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 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 16 COAT PROTEIN
1
285Human rhinovirus 16EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 16 COAT PROTEIN
2
261Human rhinovirus 16EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 16 COAT PROTEIN
3
238Human rhinovirus 16EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 16 COAT PROTEIN
4
68Human rhinovirus 1AEC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P23008 (Human rhinovirus 1A)
Go to UniProtKB:  P23008
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
4
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
1
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.230 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 362.600α = 90.00
b = 347.100β = 90.00
c = 334.900γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing
DENZOdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance