6E5U

Crystal structure of the mRNA export receptor NXF1/NXT1 in complex with influenza virus NS1 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for influenza virus NS1 protein block of mRNA nuclear export.

Zhang, K.Xie, Y.Munoz-Moreno, R.Wang, J.Zhang, L.Esparza, M.Garcia-Sastre, A.Fontoura, B.M.A.Ren, Y.

(2019) Nat Microbiol 4: 1671-1679

  • DOI: 10.1038/s41564-019-0482-x
  • Primary Citation of Related Structures:  
    6E5U

  • PubMed Abstract: 
  • Influenza viruses antagonize key immune defence mechanisms via the virulence factor non-structural protein 1 (NS1). A key mechanism of virulence by NS1 is blocking nuclear export of host messenger RNAs, including those encoding immune factors 1-3 ; however, the direct cellular target of NS1 and the mechanism of host mRNA export inhibition are not known ...

    Influenza viruses antagonize key immune defence mechanisms via the virulence factor non-structural protein 1 (NS1). A key mechanism of virulence by NS1 is blocking nuclear export of host messenger RNAs, including those encoding immune factors 1-3 ; however, the direct cellular target of NS1 and the mechanism of host mRNA export inhibition are not known. Here, we identify the target of NS1 as the mRNA export receptor complex, nuclear RNA export factor 1-nuclear transport factor 2-related export protein 1 (NXF1-NXT1), which is the principal receptor mediating docking and translocation of mRNAs through the nuclear pore complex via interactions with nucleoporins 4,5 . We determined the crystal structure of NS1 in complex with NXF1-NXT1 at 3.8 Å resolution. The structure reveals that NS1 prevents binding of NXF1-NXT1 to nucleoporins, thereby inhibiting mRNA export through the nuclear pore complex into the cytoplasm for translation. We demonstrate that a mutant influenza virus deficient in binding NXF1-NXT1 does not block host mRNA export and is attenuated. This attenuation is marked by the release of mRNAs encoding immune factors from the nucleus. In sum, our study uncovers the molecular basis of a major nuclear function of influenza NS1 protein that causes potent blockage of host gene expression and contributes to inhibition of host immunity.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA. yi.ren@vanderbilt.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear RNA export factor 1A, C, E, G508Homo sapiensMutation(s): 0 
Gene Names: NXF1TAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBU9 (Homo sapiens)
Explore Q9UBU9 
Go to UniProtKB:  Q9UBU9
PHAROS:  Q9UBU9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NTF2-related export protein 1B, D, F, H140Homo sapiensMutation(s): 0 
Gene Names: NXT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKK6 (Homo sapiens)
Explore Q9UKK6 
Go to UniProtKB:  Q9UKK6
PHAROS:  Q9UKK6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 1P [auth J], I [auth K], J [auth L], K [auth M]77Influenza A virusMutation(s): 2 
Gene Names: NS1NS
UniProt
Find proteins for I7CAR2 (Influenza A virus)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 1L [auth U], M [auth V], N [auth X], O [auth Y]153Influenza A virusMutation(s): 1 
Gene Names: NS1NS
UniProt
Find proteins for I7CAR2 (Influenza A virus)
Explore I7CAR2 
Go to UniProtKB:  I7CAR2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.905α = 90
b = 101.905β = 90
c = 949.476γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-07-23 
  • Released Date: 2019-04-24 
  • Deposition Author(s): Xie, Y., Ren, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references