4AED

Crystal structure of Human enterovirus 71

PDB DOI: https://doi.org/10.2210/pdb4AED/pdb

Classification: VIRUS
Organism(s): Enterovirus A71
Mutation(s): No

Deposited: 2012-01-09 Released: 2012-04-25
Deposition Author(s): Plevka, P., Perera, R., Kuhn, R.J., Rossmann, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Work: 0.279
R-Value Observed: 0.279

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Human Enterovirus 71.

Plevka, P., Perera, R., Cardosa, J., Kuhn, R.J., Rossmann, M.G.

(2012) Science 336: 1274

PubMed: 22383808 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1218713
Primary Citation of Related Structures:
4AED

PubMed Abstract:
Enterovirus 71 is a picornavirus associated with fatal neurological illness in infants and young children. Here, we report the crystal structure of enterovirus 71 and show that, unlike in other enteroviruses, the "pocket factor," a small molecule that stabilizes the virus, is partly exposed on the floor of the "canyon." Thus, the structure of antiviral compounds may require a hydrophilic head group designed to interact with residues at the entrance of the pocket.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 95 kDa
Atom Count: 6,471
Modelled Residue Count: 831
Deposited Residue Count: 862
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	297	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for A9X4C2 (Human enterovirus 71) Explore A9X4C2 Go to UniProtKB: A9X4C2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9X4C2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B	254	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for A9X4C2 (Human enterovirus 71) Explore A9X4C2 Go to UniProtKB: A9X4C2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9X4C2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C	242	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for A9X4C2 (Human enterovirus 71) Explore A9X4C2 Go to UniProtKB: A9X4C2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9X4C2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VP4	D	69	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for A9X4C2 (Human enterovirus 71) Explore A9X4C2 Go to UniProtKB: A9X4C2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9X4C2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAO Query on DAO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C]	F [auth B], G [auth B], H [auth C], I [auth C], J [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Work: 0.279
R-Value Observed: 0.279
Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 600.2	α = 90
b = 610.6	β = 90
c = 851.8	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing
PHASER	phasing
GLRF	phasing
CCP4	phasing
USF	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 2012-06-20
Changes: Other
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description