4U2X

Ebola virus VP24 in complex with Karyopherin alpha 5 C-terminus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Ebola Virus VP24 Targets a Unique NLS Binding Site on Karyopherin Alpha 5 to Selectively Compete with Nuclear Import of Phosphorylated STAT1.

Xu, W., Edwards, M.R., Borek, D.M., Feagins, A.R., Mittal, A., Alinger, J.B., Berry, K.N., Yen, B., Hamilton, J., Brett, T.J., Pappu, R.V., Leung, D.W., Basler, C.F., Amarasinghe, G.K.

(2014) Cell Host Microbe 16: 187-200

  • DOI: https://doi.org/10.1016/j.chom.2014.07.008
  • Primary Citation of Related Structures:  
    4U2X

  • PubMed Abstract: 

    • During antiviral defense, interferon (IFN) signaling triggers nuclear transport of tyrosine-phosphorylated STAT1 (PY-STAT1), which occurs via a subset of karyopherin alpha (KPNA) nuclear transporters. Many viruses, including Ebola virus, actively antagonize STAT1 signaling to counteract the antiviral effects of IFN ...

    During antiviral defense, interferon (IFN) signaling triggers nuclear transport of tyrosine-phosphorylated STAT1 (PY-STAT1), which occurs via a subset of karyopherin alpha (KPNA) nuclear transporters. Many viruses, including Ebola virus, actively antagonize STAT1 signaling to counteract the antiviral effects of IFN. Ebola virus VP24 protein (eVP24) binds KPNA to inhibit PY-STAT1 nuclear transport and render cells refractory to IFNs. We describe the structure of human KPNA5 C terminus in complex with eVP24. In the complex, eVP24 recognizes a unique nonclassical nuclear localization signal (NLS) binding site on KPNA5 that is necessary for efficient PY-STAT1 nuclear transport. eVP24 binds KPNA5 with very high affinity to effectively compete with and inhibit PY-STAT1 nuclear transport. In contrast, eVP24 binding does not affect the transport of classical NLS cargo. Thus, eVP24 counters cell-intrinsic innate immunity by selectively targeting PY-STAT1 nuclear import while leaving the transport of other cargo that may be required for viral replication unaffected.

    Organizational Affiliation: 

    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA. Electronic address: gamarasinghe@path.wustl.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Membrane-associated protein VP24A, B, C216Ebola virus - Mayinga, Zaire, 1976Mutation(s): 0 
Gene Names: VP24
Membrane Entity: Yes 
UniProt
Find proteins for Q05322 (Zaire ebolavirus (strain Mayinga-76))
Explore Q05322 
Go to UniProtKB:  Q05322
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05322
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Importin subunit alpha-6D, E, F175Homo sapiensMutation(s): 0 
Gene Names: KPNA5
UniProt & NIH Common Fund Data Resources
Find proteins for O15131 (Homo sapiens)
Explore O15131 
Go to UniProtKB:  O15131
PHAROS:  O15131
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15131
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.925α = 90
b = 103.925β = 90
c = 333.63γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI107056
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI081914

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence