4Q4X

Crystal structure of Coxsackievirus A24v soaked with 6'-Sialyllactose (6SL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A sialic Acid binding site in a human picornavirus.

Zocher, G.Mistry, N.Frank, M.Hahnlein-Schick, I.Ekstrom, J.O.Arnberg, N.Stehle, T.

(2014) Plos Pathog. 10: e1004401-e1004401

  • DOI: 10.1371/journal.ppat.1004401
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The picornaviruses coxsackievirus A24 variant (CVA24v) and enterovirus 70 (EV70) cause continued outbreaks and pandemics of acute hemorrhagic conjunctivitis (AHC), a highly contagious eye disease against which neither vaccines nor antiviral drugs are ...

    The picornaviruses coxsackievirus A24 variant (CVA24v) and enterovirus 70 (EV70) cause continued outbreaks and pandemics of acute hemorrhagic conjunctivitis (AHC), a highly contagious eye disease against which neither vaccines nor antiviral drugs are currently available. Moreover, these viruses can cause symptoms in the cornea, upper respiratory tract, and neurological impairments such as acute flaccid paralysis. EV70 and CVA24v are both known to use 5-N-acetylneuraminic acid (Neu5Ac) for cell attachment, thus providing a putative link between the glycan receptor specificity and cell tropism and disease. We report the structures of an intact human picornavirus in complex with a range of glycans terminating in Neu5Ac. We determined the structure of the CVA24v to 1.40 Å resolution, screened different glycans bearing Neu5Ac for CVA24v binding, and structurally characterized interactions with candidate glycan receptors. Biochemical studies verified the relevance of the binding site and demonstrated a preference of CVA24v for α2,6-linked glycans. This preference can be rationalized by molecular dynamics simulations that show that α2,6-linked glycans can establish more contacts with the viral capsid. Our results form an excellent platform for the design of antiviral compounds to prevent AHC.


    Organizational Affiliation

    Interfaculty Institute of Biochemistry, University Tübingen, Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coxsackievirus capsid protein VP1
1
305Coxsackievirus A24Mutation(s): 0 
Find proteins for V9VEF3 (Coxsackievirus A24)
Go to UniProtKB:  V9VEF3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coxsackievirus capsid protein VP2
2
271Coxsackievirus A24Mutation(s): 0 
Find proteins for V9VEF3 (Coxsackievirus A24)
Go to UniProtKB:  V9VEF3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Coxsackievirus capsid protein VP3
3
240Coxsackievirus A24Mutation(s): 0 
Find proteins for V9VEF3 (Coxsackievirus A24)
Go to UniProtKB:  V9VEF3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Coxsackievirus capsid protein VP4
4
69Coxsackievirus A24Mutation(s): 0 
Find proteins for V9VEF3 (Coxsackievirus A24)
Go to UniProtKB:  V9VEF3
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download SDF File 
Download CCD File 
1
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
1
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
1, 2, 3
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
1, 2, 3
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
1
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Work: 0.149 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 306.398α = 90.00
b = 366.096β = 90.00
c = 367.700γ = 90.00
Software Package:
Software NamePurpose
PYMOLmodel building
REFMACrefinement
XDSdata reduction
PYMOLphasing
XSCALEdata scaling
ISPyBdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-04-15 
  • Released Date: 2014-11-05 
  • Deposition Author(s): Zocher, G., Stehle, T.

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release