4WM8

Crystal Structure of Human Enterovirus D68


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Virus structure. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children.

Liu, Y.Sheng, J.Fokine, A.Meng, G.Shin, W.H.Long, F.Kuhn, R.J.Kihara, D.Rossmann, M.G.

(2015) Science 347: 71-74

  • DOI: 10.1126/science.1261962
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enterovirus D68 (EV-D68) is a member of Picornaviridae and is a causative agent of recent outbreaks of respiratory illness in children in the United States. We report here the crystal structures of EV-D68 and its complex with pleconaril, a capsid-bin ...

    Enterovirus D68 (EV-D68) is a member of Picornaviridae and is a causative agent of recent outbreaks of respiratory illness in children in the United States. We report here the crystal structures of EV-D68 and its complex with pleconaril, a capsid-binding compound that had been developed as an anti-rhinovirus drug. The hydrophobic drug-binding pocket in viral protein 1 contained density that is consistent with a fatty acid of about 10 carbon atoms. This density could be displaced by pleconaril. We also showed that pleconaril inhibits EV-D68 at a half-maximal effective concentration of 430 nanomolar and might, therefore, be a possible drug candidate to alleviate EV-D68 outbreaks.


    Organizational Affiliation

    Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA. Department of Computer Science, 305 North University Street, Purdue University, West Lafayette, IN 47907, USA.,Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA. mr@purdue.edu.,Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
297Human enterovirus D68Mutation(s): 0 
Gene Names: VP1
Find proteins for Q9YLJ3 (Human enterovirus D68)
Go to UniProtKB:  Q9YLJ3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP2
B
248Human enterovirus D68Mutation(s): 0 
Find proteins for Q68T42 (Human enterovirus D68)
Go to UniProtKB:  Q68T42
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
C
247Human enterovirus D68Mutation(s): 0 
Find proteins for Q68T42 (Human enterovirus D68)
Go to UniProtKB:  Q68T42
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP4
D
68Human enterovirus D68Mutation(s): 0 
Find proteins for Q8QWD4 (Human enterovirus D68)
Go to UniProtKB:  Q8QWD4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DKA
Query on DKA

Download SDF File 
Download CCD File 
A
DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.275 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 327.000α = 90.00
b = 347.800β = 90.00
c = 357.100γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
CNSrefinement
HKL-3000phasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI11219

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-11
    Type: Author supporting evidence