1D4M

THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of coxsackievirus A9: new insights into the uncoating mechanisms of enteroviruses.

Hendry, E.Hatanaka, H.Fry, E.Smyth, M.Tate, J.Stanway, G.Santti, J.Maaronen, M.Hyypia, T.Stuart, D.

(1999) Structure 7: 1527-1538

  • DOI: https://doi.org/10.1016/s0969-2126(00)88343-4
  • Primary Citation of Related Structures:  
    1D4M

  • PubMed Abstract: 

    Coxsackievirus A9 (CAV9), a human pathogen causing symptoms ranging from common colds to fatal infections of the central nervous system, is an icosahedral single-stranded RNA virus that belongs to the genus Enterovirus of the family Picornaviridae. One of the four capsid proteins, VP1, includes the arginine-glycine-aspartate (RGD) motif within its C-terminal extension. This region binds to integrin alpha v beta 3, the only receptor for CAV9 to be conclusively identified to date. The crystal structure of CAV9 in complex with the antiviral compound WIN 51711 has been solved to 2.9 A resolution. The structures of the four capsid proteins, VP1 to VP4, resemble those of other picornaviruses. The antiviral compound is bound in the VP1 hydrophobic pocket, and it is possible that the pocket entrance contains a second WIN 51711 molecule. Continuous electron density for the VP1 N terminus provides a complete picture of the structure close to the fivefold axis. The VP1 C-terminal portion is on the outer surface of the virus and becomes disordered five-residues N-terminal to the RGD motif. The RGD motif is exposed and flexible in common with other known integrin ligands. Although CAV9 resembles coxsackie B viruses (CBVs), several substitutions in the areas implicated in CBV receptor attachment suggest it may recognise a different receptor. The structure along the fivefold axis provides new information on the uncoating mechanism of enteroviruses. CAV9 might bind a larger natural pocket factor than other picornaviruses, an observation of particular relevance to the design of new antiviral compounds.


  • Organizational Affiliation

    Laboratory of Molecular Biophysics, Oxford, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (COXSACKIEVIRUS A9)A [auth 1]299Coxsackievirus A9Mutation(s): 0 
UniProt
Find proteins for P21404 (Coxsackievirus A9 (strain Griggs))
Explore P21404 
Go to UniProtKB:  P21404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21404
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (COXSACKIEVIRUS A9)B [auth 2]261Coxsackievirus A9Mutation(s): 0 
UniProt
Find proteins for P21404 (Coxsackievirus A9 (strain Griggs))
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Go to UniProtKB:  P21404
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UniProt GroupP21404
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (COXSACKIEVIRUS A9)C [auth 3]238Coxsackievirus A9Mutation(s): 0 
UniProt
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Go to UniProtKB:  P21404
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UniProt GroupP21404
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (COXSACKIEVIRUS A9)D [auth 4]68Coxsackievirus A9Mutation(s): 0 
UniProt
Find proteins for P21404 (Coxsackievirus A9 (strain Griggs))
Explore P21404 
Go to UniProtKB:  P21404
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UniProt GroupP21404
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W71
Query on W71

Download Ideal Coordinates CCD File 
E [auth 1],
F [auth 1]
5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE
C20 H26 N2 O3
FKLJPTJMIBLJAV-UHFFFAOYSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
G [auth 4]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 487.3α = 90
b = 358.1β = 128.1
c = 305.7γ = 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: 1999-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-05-31
    Changes: Database references, Derived calculations