8VPU

Crystal structure of mouse Importin alpha in complex with dengue virus 3 NS5 central NLS peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Serotype-Specific Regulation of Dengue Virus NS5 Protein Subcellular Localization.

Cheng, C.X.Tan, M.J.A.Chan, K.W.K.Choy, M.M.J.Roman, N.Arnold, D.D.R.Bifani, A.M.Kong, S.Y.Z.Bist, P.Nath, B.K.Swarbrick, C.M.D.Forwood, J.K.Vasudevan, S.G.

(2024) ACS Infect Dis 10: 2047-2062

  • DOI: https://doi.org/10.1021/acsinfecdis.4c00054
  • Primary Citation of Related Structures:  
    8VPR, 8VPU

  • PubMed Abstract: 

    Dengue virus (DENV) nonstructural protein 5 (NS5), consisting of methyltransferase and RNA-dependent RNA polymerase (RdRp) domains, is critical for viral RNA synthesis within endoplasmic reticulum-derived replication complexes in the cytoplasm. However, a significant proportion of NS5 is localized to the nucleus of infected cells for DENV2, 3, and 4, whereas DENV1 NS5 is localized diffusely in the cytoplasm. We still have an incomplete understanding of how the DENV NS5 subcellular localization is regulated. Within NS5, two putative nuclear localization signal (NLS) sequences have been identified: NLS Central residing in the palm of the RdRp domain as well as the recently discovered NLS C-term residing in the flexible region at the C-terminal of the RdRp domain. We have previously shown that DENV2 NS5 nuclear localization can be significantly reduced by single-point mutations to the NLS C-term . Here, we present biochemical, virological, and structural data demonstrating that the relative importance of either NLS in NS5 nuclear localization is unique to each of the four DENV serotypes. DENV1 NS5's cytoplasmic localization appears to be due to a functionally weak interaction between its NLS Central and importin-α (IMPα), while DENV2 NS5 is almost exclusively nuclear through its NLS C-term 's strong interaction with IMPα. Both NLSs of DENV3 NS5 appear to contribute to directing its nuclear localization. Lastly, in the case of DENV4, the regulation of its NS5 nuclear localization remains an enigma but appears to be associated with its NLS C-term .


  • Organizational Affiliation

    Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Importin subunit alpha-1510Mus musculusMutation(s): 0 
Gene Names: Kpna2Rch1
UniProt & NIH Common Fund Data Resources
Find proteins for P52293 (Mus musculus)
Explore P52293 
Go to UniProtKB:  P52293
IMPC:  MGI:103561
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52293
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase NS5 central NLS peptide37dengue virus type 3Mutation(s): 0 
Gene Names: POLY
UniProt
Find proteins for A9LID6 (dengue virus type 3)
Explore A9LID6 
Go to UniProtKB:  A9LID6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9LID6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.92α = 90
b = 89.44β = 90
c = 100.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF2016-CRP001-063

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release