4N53

Human enterovirus 71 uncoating intermediate captured at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3063 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Human enterovirus 71 uncoating captured at atomic resolution.

Lyu, K.Ding, J.Han, J.F.Zhang, Y.Wu, X.Y.He, Y.L.Qin, C.F.Chen, R.

(2014) J.Virol. 88: 3114-3126

  • DOI: 10.1128/JVI.03029-13
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human enterovirus 71 (EV71) is the major causative agent of severe hand-foot-and-mouth diseases (HFMD) in young children, and structural characterization of EV71 during its life cycle can aid in the development of therapeutics against HFMD. Here, we ...

    Human enterovirus 71 (EV71) is the major causative agent of severe hand-foot-and-mouth diseases (HFMD) in young children, and structural characterization of EV71 during its life cycle can aid in the development of therapeutics against HFMD. Here, we present the atomic structures of the full virion and an uncoating intermediate of a clinical EV71 C4 strain to illustrate the structural changes in the full virion that lead to the formation of the uncoating intermediate prepared for RNA release. Although the VP1 N-terminal regions observed to penetrate through the junction channel at the quasi-3-fold axis in the uncoating intermediate of coxsackievirus A16 were not observed in the EV71 uncoating intermediate, drastic conformational changes occur in this region, as has been observed in all capsid proteins. Additionally, the RNA genome interacts with the N-terminal extensions of VP1 and residues 32 to 36 of VP3, both of which are situated at the bottom of the junction. These observations highlight the importance of the junction for genome release. Furthermore, EV71 uncoating is associated with apparent rearrangements and expansion around the 2- and 5-fold axes without obvious changes around the 3-fold axes. Therefore, these structures enabled the identification of hot spots for capsid rearrangements, which led to the hypothesis that the protomer interface near the junction and the 2-fold axis permits the opening of large channels for the exit of polypeptides and viral RNA, which is an uncoating mechanism that is likely conserved in enteroviruses.


    Organizational Affiliation

    Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A
297Enterovirus A71Mutation(s): 0 
Find proteins for S5QA87 (Enterovirus A71)
Go to UniProtKB:  S5QA87
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2
B
254Enterovirus A71Mutation(s): 0 
Find proteins for S4VM80 (Enterovirus A71)
Go to UniProtKB:  S4VM80
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP3
C
242Enterovirus A71Mutation(s): 0 
Find proteins for S5ZCI0 (Enterovirus A71)
Go to UniProtKB:  S5ZCI0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP4
D
69Enterovirus A71Mutation(s): 0 
Find proteins for S6C3M9 (Enterovirus A71)
Go to UniProtKB:  S6C3M9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPH
Query on SPH

Download SDF File 
Download CCD File 
A
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3063 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 591.375α = 90.00
b = 591.375β = 90.00
c = 591.375γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-09 
  • Released Date: 2014-02-05 
  • Deposition Author(s): Chen, R., Lyu, K.

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references