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 

Starting Model: experimental
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This is version 2.2 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

  • DOI: https://doi.org/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 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. The structure of native HRV16 has been refined to a resolution of 2.15 A. The hydrophobic pocket in VP1 is observed in two alternative conformations. In one of these, the pocket is filled by a pocket factor and the protein structure is similar to virus-antiviral compound complexes. In the other conformation, the hydrophobic pocket is collapsed and empty. RNA bases stack against both a tryptophan and a phenylalanine residue on the internal surface of the viral capsid. Site-directed mutagenesis of the tryptophan, which is conserved across the picornaviruses, to nonconservative residues results in non-viable virus. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel beta barrel around the base of the icosahedral fivefold axis. The N termini of VP1 are amphipathic alpha helices, which stack on the outside of this beta barrel. The N termini of VP1 and VP4 have not been observed previously in rhinovirus structures. The observation of a partially occupied hydrophobic pocket in HRV16 forms a missing link between HRV14, which is always observed with no pocket factor in the native form, and rhinovirus 1A and other picornaviruses (e.g. poliovirus, coxsackievirus) which contain pocket factors. The pocket factor molecules probably regulate viral entry, uncoating and assembly. Picornavirus assembly is known to proceed via pentamers, therefore, the interaction of RNA with the conserved tryptophan residues across twofold axes between pentamers may play a role in picornavirus assembly. The positioning of a cation on the icosahedral fivefold axes and the structure of the N termini of VP4 and VP1 around these axes suggest a mechanism for the uncoating of rhinoviruses.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 16 COAT PROTEINA [auth 1]285Human rhinovirus sp.Mutation(s): 0 
UniProt
Find proteins for Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
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UniProt GroupQ82122
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 16 COAT PROTEINB [auth 2]261Human rhinovirus sp.Mutation(s): 0 
UniProt
Find proteins for Q82122 (Human rhinovirus 16)
Explore Q82122 
Go to UniProtKB:  Q82122
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UniProt GroupQ82122
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 16 COAT PROTEINC [auth 3]238Human rhinovirus sp.Mutation(s): 0 
UniProt
Find proteins for Q82122 (Human rhinovirus 16)
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Go to UniProtKB:  Q82122
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UniProt GroupQ82122
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 16 COAT PROTEIND [auth 4]68Human rhinovirus sp.Mutation(s): 0 
UniProt
Find proteins for P23008 (Human rhinovirus 1A)
Explore P23008 
Go to UniProtKB:  P23008
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2023-02-08
    Type: Remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2023-03-15
    Changes: Advisory
  • Version 2.2: 2023-08-09
    Changes: Refinement description