4WM8 | pdb_00004wm8

Crystal Structure of Human Enterovirus D68

PDB DOI: https://doi.org/10.2210/pdb4WM8/pdb

Classification: VIRUS
Organism(s): enterovirus D68
Mutation(s): No

Deposited: 2014-10-08 Released: 2015-01-14
Deposition Author(s): Liu, Y., Sheng, J., Fokine, A., Meng, G., Long, F., Kuhn, R.J., Rossmann, M.G.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.279 (Depositor), 0.256 (DCC)
R-Value Work:
0.275 (Depositor), 0.256 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 25554786 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1261962
Primary Citation Related Structures:
4WM7, 4WM8

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-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.

Macromolecule Content

Total Structure Weight: 95.2 kDa
Atom Count: 6,493
Modeled Residue Count: 805
Deposited Residue Count: 860
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	297	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q9YLJ3 (Human enterovirus D68) Explore Q9YLJ3 Go to UniProtKB: Q9YLJ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9YLJ3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B	248	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42 Go to UniProtKB: Q68T42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q68T42
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C	247	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42 Go to UniProtKB: Q68T42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q68T42
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VP4	D	68	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q8QWD4 (Human enterovirus D68) Explore Q8QWD4 Go to UniProtKB: Q8QWD4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8QWD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DKA Query on DKA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DECANOIC ACID C₁₀ H₂₀ O₂ GHVNFZFCNZKVNT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.279 (Depositor), 0.256 (DCC)
R-Value Work: 0.275 (Depositor), 0.256 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 327	α = 90
b = 347.8	β = 90
c = 357.1	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-3000	phasing
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI11219

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2015-02-25
Changes: Database references
Version 1.2: 2017-09-20
Changes: Author supporting evidence, Database references, Other, Refinement description, Source and taxonomy
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description