3VBF

Crystal structure of formaldehyde treated human Enterovirus 71 (space group I23)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.

Wang, X.Peng, W.Ren, J.Hu, Z.Xu, J.Lou, Z.Li, X.Yin, W.Shen, X.Porta, C.Walter, T.S.Evans, G.Axford, D.Owen, R.Rowlands, D.J.Wang, J.Stuart, D.I.Fry, E.E.Rao, Z.

(2012) Nat Struct Mol Biol 19: 424-429

  • DOI: https://doi.org/10.1038/nsmb.2255
  • Primary Citation of Related Structures:  
    3VBF, 3VBH, 3VBO, 3VBR, 3VBS, 3VBU

  • PubMed Abstract: 

    Enterovirus 71 (EV71) is a major agent of hand, foot and mouth disease in children that can cause severe central nervous system disease and death. No vaccine or antiviral therapy is available. High-resolution structural analysis of the mature virus and natural empty particles shows that the mature virus is structurally similar to other enteroviruses. In contrast, the empty particles are markedly expanded and resemble elusive enterovirus-uncoating intermediates not previously characterized in atomic detail. Hydrophobic pockets in the EV71 capsid are collapsed in this expanded particle, providing a detailed explanation of the mechanism for receptor-binding triggered virus uncoating. These structures provide a model for enterovirus uncoating in which the VP1 GH loop acts as an adaptor-sensor for cellular receptor attachment, converting heterologous inputs to a generic uncoating mechanism, highlighting new opportunities for therapeutic intervention.


  • Organizational Affiliation

    National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome Polyprotein, capsid protein VP1297Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Genome Polyprotein, capsid protein VP2245Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Genome Polyprotein, capsid protein VP3242Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Genome Polyprotein, capsid protein VP458Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B2ZUN0 (Human enterovirus 71)
Explore B2ZUN0 
Go to UniProtKB:  B2ZUN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZUN0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
F [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
SPH
Query on SPH

Download Ideal Coordinates CCD File 
E [auth A]SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
K
Query on K

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G [auth A],
I [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 600.1α = 90
b = 600.1β = 90
c = 600.1γ = 90
Software Package:
Software NamePurpose
GDAdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2012-04-25
    Changes: Database references
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description