7RFY

Importin alpha3 in complex with MERS ORF4B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

MERS-CoV ORF4b employs an unusual binding mechanism to target IMP alpha and block innate immunity.

Munasinghe, T.S.Edwards, M.R.Tsimbalyuk, S.Vogel, O.A.Smith, K.M.Stewart, M.Foster, J.K.Bosence, L.A.Aragao, D.Roby, J.A.Basler, C.F.Forwood, J.K.

(2022) Nat Commun 13: 1604-1604

  • DOI: https://doi.org/10.1038/s41467-022-28851-2
  • Primary Citation of Related Structures:  
    7RFX, 7RFY, 7RFZ, 7RG0, 7RG2, 7RG3, 7RG4, 7RG5, 7RG6

  • PubMed Abstract: 

    The MERS coronavirus (MERS-CoV) is a highly pathogenic, emerging virus that produces accessory proteins to antagonize the host innate immune response. The MERS-CoV ORF4b protein has been shown to bind preferentially to the nuclear import adapter IMPα3 in infected cells, thereby inhibiting NF-κB-dependent innate immune responses. Here, we report high-resolution structures of ORF4b bound to two distinct IMPα family members. Each exhibit highly similar binding mechanisms that, in both cases, lack a prototypical Lys bound at their P2 site. Mutations within the NLS region dramatically alter the mechanism of binding, which reverts to the canonical P2 Lys binding mechanism. Mutational studies confirm that the novel binding mechanism is important for its nuclear import, IMPα interaction, and inhibition of innate immune signaling pathways. In parallel, we determined structures of the nuclear binding domain of NF-κB component p50 bound to both IMPα2 and α3, demonstrating that p50 overlaps with the ORF4b binding sites, suggesting a basis for inhibition. Our results provide a detailed structural basis that explains how a virus can target the IMPα nuclear import adapter to impair immunity, and illustrate how small mutations in ORF4b, like those found in closely related coronaviruses such as HKU5, change the IMPα binding mechanism.


  • Organizational Affiliation

    School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Importin subunit alpha-3459Homo sapiensMutation(s): 0 
Gene Names: KPNA4QIP1
UniProt & NIH Common Fund Data Resources
Find proteins for O00629 (Homo sapiens)
Explore O00629 
Go to UniProtKB:  O00629
PHAROS:  O00629
GTEx:  ENSG00000186432 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00629
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ORF4b21Middle East respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for K9N643 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N643 
Go to UniProtKB:  K9N643
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N643
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.222α = 90
b = 59.711β = 98.89
c = 82.64γ = 90
Software Package:
Software NamePurpose
autoBUSTERphasing
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP2003636

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description