4U2X | pdb_00004u2x

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 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4U2X

This is version 1.6 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 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. 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.

Macromolecule Content 

  • Total Structure Weight: 131.77 kDa 
  • Atom Count: 9,199 
  • Modeled Residue Count: 1,162 
  • Deposited Residue Count: 1,173 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane-associated protein VP24
A, B, C
216Ebola 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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin subunit alpha-6
D, E, F
175Homo 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
GTEx:  ENSG00000196911 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15131
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.249 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
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

View Full Validation Report



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
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2024-10-30
    Changes: Structure summary