2IJO

Crystal Structure of the West Nile virus NS2B-NS3 protease complexed with bovine pancreatic trypsin inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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This is version 1.3 of the entry. See complete history. 


Literature

Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold.

Aleshin, A.E., Shiryaev, S.A., Strongin, A.Y., Liddington, R.C.

(2007) Protein Sci 16: 795-806

  • DOI: 10.1110/ps.072753207
  • Primary Citation of Related Structures:  
    2GGV, 2IJO

  • PubMed Abstract: 

    • Pathogenic members of the flavivirus family, including West Nile Virus (WNV) and Dengue Virus (DV), are growing global threats for which there are no specific treatments. The two-component flaviviral enzyme NS2B-NS3 cleaves the viral polyprotein precursor within the host cell, a process that is required for viral replication ...

    Pathogenic members of the flavivirus family, including West Nile Virus (WNV) and Dengue Virus (DV), are growing global threats for which there are no specific treatments. The two-component flaviviral enzyme NS2B-NS3 cleaves the viral polyprotein precursor within the host cell, a process that is required for viral replication. Here, we report the crystal structure of WNV NS2B-NS3pro both in a substrate-free form and in complex with the trypsin inhibitor aprotinin/BPTI. We show that aprotinin binds in a substrate-mimetic fashion in which the productive conformation of the protease is fully formed, providing evidence for an "induced fit" mechanism of catalysis and allowing us to rationalize the distinct substrate specificities of WNV and DV proteases. We also show that the NS2B cofactor of WNV can adopt two very distinct conformations and that this is likely to be a general feature of flaviviral proteases, providing further opportunities for regulation. Finally, by comparing the flaviviral proteases with the more distantly related Hepatitis C virus, we provide insights into the evolution of the Flaviviridae fold. Our work should expedite the design of protease inhibitors to treat a range of flaviviral infections.

    Organizational Affiliation: 

    Infectious and Inflammatory Disease Center, Burnham Institute for Medical Research, La Jolla, California 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinA58West Nile virusMutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P06935 (West Nile virus)
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Go to UniProtKB:  P06935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06935
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinB192West Nile virusMutation(s): 2 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P06935 (West Nile virus)
Explore P06935 
Go to UniProtKB:  P06935
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UniProt GroupP06935
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pancreatic trypsin inhibitorC [auth I]58Bos taurusMutation(s): 0 
UniProt
Find proteins for P00974 (Bos taurus)
Explore P00974 
Go to UniProtKB:  P00974
Entity Groups  
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UniProt GroupP00974
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.05α = 90
b = 72.177β = 90
c = 79.417γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references