4N53

Human enterovirus 71 uncoating intermediate captured at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1A297Enterovirus A71Mutation(s): 0 
Find proteins for S5QA87 (Human enterovirus 71)
Explore S5QA87 
Go to UniProtKB:  S5QA87
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2B254Enterovirus A71Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for S4VM80 (Human enterovirus 71)
Explore S4VM80 
Go to UniProtKB:  S4VM80
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP3C242Enterovirus A71Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for S5ZCI0 (Human enterovirus 71)
Explore S5ZCI0 
Go to UniProtKB:  S5ZCI0
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP4D69Enterovirus A71Mutation(s): 0 
Find proteins for S6C3M9 (Human enterovirus 71)
Explore S6C3M9 
Go to UniProtKB:  S6C3M9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPH
Query on SPH

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 591.375α = 90
b = 591.375β = 90
c = 591.375γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

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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
    Changes: Database references