1AYN

HUMAN RHINOVIRUS 16 COAT PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.Rossman, M.G.

(1993) Structure 1: 51-68

  • Also Cited By: 1QJU, 1QJX, 1QJY

  • PubMed Abstract: 
  • Rhinoviruses and the homologous polioviruses have hydrophobic pockets below their receptor-binding sites, which often contain unidentified electron density ('pocket factors'). Certain antiviral compounds also bind in the pocket, displacing the pocket ...

    Rhinoviruses and the homologous polioviruses have hydrophobic pockets below their receptor-binding sites, which often contain unidentified electron density ('pocket factors'). Certain antiviral compounds also bind in the pocket, displacing the pocket factor and inhibiting uncoating. However, human rhinovirus (HRV)14, which belongs to the major group of rhinoviruses that use intercellular adhesion molecule-1 (ICAM-1) as a receptor, has an empty pocket. When antiviral compounds bind into the empty pocket of HRV14, the roof of the pocket, which is also the floor of the receptor binding site (the canyon), is deformed, preventing receptor attachment. The role of the pocket in viral infectivity is not known.


    Related Citations: 
    • 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
    • The Refined Structure of Human Rhinovirus 16 at 2.15 Angstroms Resolution: Implications for the Viral Life Cycle
      Hadfield, A.T.,Lee, W.M.,Zhao, R.,Oliveira, M.A.,Minor, I.,Rueckert, R.R.,Rossmann, M.G.
      (1997) Structure 5: 427
    • 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
    • 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
    • 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


    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 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: 2.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.229 
  • 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
X-PLORmodel building
PURDUEdata scaling
X-PLORrefinement
PURDUEdata reduction
X-PLORphasing

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
  • Version 1.3: 2012-02-29
    Type: Database references