3QZR

Human enterovirus 71 3C protease mutant E71A in complex with rupintrivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of Enterovirus 71 3C Protease Complexed with Rupintrivir Reveal the Roles of Catalytically Important Residues.

Wang, J.Fan, T.Yao, X.Wu, Z.Guo, L.Lei, X.Wang, J.Wang, M.Jin, Q.Cui, S.

(2011) J Virol 85: 10021-10030

  • DOI: https://doi.org/10.1128/JVI.05107-11
  • Primary Citation of Related Structures:  
    3QZQ, 3QZR, 3R0F

  • PubMed Abstract: 

    EV71 is the primary pathogenic cause of hand-foot-mouth disease (HFMD), but an effective antiviral drug currently is unavailable. Rupintrivir, an inhibitor against human rhinovirus (HRV), has potent antiviral activities against EV71. We determined the high-resolution crystal structures of the EV71 3C(pro)/rupintrivir complex, showing that although rupintrivir interacts with EV71 3C(pro) similarly to HRV 3C(pro), the C terminus of the inhibitor cannot accommodate the leaving-group pockets of EV71 3C(pro). Our structures reveal that EV71 3C(pro) possesses a surface-recessive S2' pocket that is not present in HRV 3C(pro) that contributes to the additional substrate binding affinity. Combined with mutagenic studies, we demonstrated that catalytic Glu71 is irreplaceable for maintaining the overall architecture of the active site and, most importantly, the productive conformation of catalytic His40. We discovered the role of a previously uncharacterized residue, Arg39 of EV71 3C(pro), that can neutralize the negative charge of Glu71, which may subsequently assist deprotonation of His40 during proteolysis.


  • Organizational Affiliation

    Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C protein
A, B
187Enterovirus A71Mutation(s): 1 
Gene Names: polyprotein
UniProt
Find proteins for E7E815 (Human enterovirus 71)
Explore E7E815 
Go to UniProtKB:  E7E815
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7E815
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.785α = 90
b = 97.822β = 90
c = 102.54γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-08-24
    Changes: Database references, Structure summary
  • Version 1.2: 2011-09-28
    Changes: Database references
  • Version 1.3: 2015-05-06
    Changes: Structure summary
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations