6JIM

Viral helicase protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase.

Law, Y.S.Utt, A.Tan, Y.B.Zheng, J.Wang, S.Chen, M.W.Griffin, P.R.Merits, A.Luo, D.

(2019) Proc Natl Acad Sci U S A 116: 9558-9567

  • DOI: 10.1073/pnas.1900656116
  • Primary Citation of Related Structures:  
    6JIM

  • PubMed Abstract: 
  • Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike ...

    Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the N-terminal RNA helicase (nsP2h) has not been determined. Here, we report the crystal structure of the nsP2h bound to the conserved 3'-end 14 nucleotides of the CHIKV genome and the nonhydrolyzable transition-state nucleotide analog ADP-AlF 4 Overall, the structural analysis revealed that nsP2h adopts a uniquely folded N-terminal domain followed by a superfamily 1 RNA helicase fold. The conserved helicase motifs establish polar contacts with the RNA backbone. There are three hydrophobic residues (Y161, F164, and F287) which form stacking interactions with RNA bases and thereby bend the RNA backbone. An F287A substitution that disrupted these stacking interactions increased the basal ATPase activity but decreased the RNA binding affinity. Furthermore, the F287A substitution reduced viral infectivity by attenuating subgenomic RNA synthesis. Replication of the mutant virus was restored by pseudoreversion (A287V) or adaptive mutations in the RecA2 helicase domain (T358S or V410I). Y161A and/or F164A substitutions, which were designed to disrupt the interactions with the RNA molecule, did not affect the ATPase activity but completely abolished the replication and transcription of viral RNA and the infectivity of CHIKV. Our study sheds light on the roles of the RNA helicase region in viral replication and provides insights that might be applicable to alphaviruses and other RNA viruses in general.


    Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
helicaseAB465Chikungunya virusMutation(s): 0 
EC: 2.7.7.19 (UniProt), 3.1.3.33 (UniProt), 3.1.3.84 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
Find proteins for A0A076V769 (synthetic recombinant Chikungunya virus strain LS3)
Explore A0A076V769 
Go to UniProtKB:  A0A076V769
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*UP*UP*UP*UP*UP)-3')C, D8Chikungunya virus
    Small Molecules
    Ligands 6 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download CCD File 
    A, B
    ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    GOL
    Query on GOL

    Download CCD File 
    A, B, C, D
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

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    A, B
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    AL
    Query on AL

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    A, B
    ALUMINUM ION
    Al
    REDXJYDRNCIFBQ-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    A, B
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    F
    Query on F

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    A, B
    FLUORIDE ION
    F
    KRHYYFGTRYWZRS-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.215 
    • R-Value Work: 0.177 
    • R-Value Observed: 0.179 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 53.888α = 96.93
    b = 53.905β = 94.07
    c = 100.718γ = 97.04
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    Aimlessdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2019-02-22 
    • Released Date: 2019-04-10 
    • Deposition Author(s): Law, Y.S.

    Funding OrganizationLocationGrant Number
    Ministry of Education (Singapore)Singapore2016T22097
    National Research Foundation (Singapore)SingaporeOFIRG17nov084

    Revision History 

    • Version 1.0: 2019-04-10
      Type: Initial release
    • Version 1.1: 2019-04-17
      Changes: Data collection, Database references
    • Version 1.2: 2019-05-01
      Changes: Data collection, Database references
    • Version 1.3: 2019-05-22
      Changes: Data collection, Database references