3KS8

Crystal structure of Reston ebolavirus VP35 RNA binding domain in complex with 18bp dsRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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This is version 1.2 of the entry. See complete history


Literature

Ebolavirus VP35 uses a bimodal strategy to bind dsRNA for innate immune suppression.

Kimberlin, C.R.Bornholdt, Z.A.Li, S.Woods, V.L.Macrae, I.J.Saphire, E.O.

(2009) Proc Natl Acad Sci U S A 107: 314-319

  • DOI: 10.1073/pnas.0910547107
  • Primary Citation of Related Structures:  
    3KS4, 3KS8

  • PubMed Abstract: 
  • Ebolavirus causes a severe hemorrhagic fever and is divided into five distinct species, of which Reston ebolavirus is uniquely nonpathogenic to humans. Disease caused by ebolavirus is marked by early immunosuppression of innate immune signaling events, involving silencing and sequestration of double-stranded RNA (dsRNA) by the viral protein VP35 ...

    Ebolavirus causes a severe hemorrhagic fever and is divided into five distinct species, of which Reston ebolavirus is uniquely nonpathogenic to humans. Disease caused by ebolavirus is marked by early immunosuppression of innate immune signaling events, involving silencing and sequestration of double-stranded RNA (dsRNA) by the viral protein VP35. Here we present unbound and dsRNA-bound crystal structures of the dsRNA-binding domain of Reston ebolavirus VP35. The structures show that VP35 forms an unusual, asymmetric dimer on dsRNA binding, with each of the monomers binding dsRNA in a different way: one binds the backbone whereas the other caps the terminus. Additional SAXS, DXMS, and dsRNA-binding experiments presented here support a model of cooperative dsRNA recognition in which binding of the first monomer assists binding of the next monomer of the oligomeric VP35 protein. This work illustrates how ebolavirus VP35 could mask key recognition sites of molecules such as RIG-I, MDA-5, and Dicer to silence viral dsRNA in infection.


    Organizational Affiliation

    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase cofactor VP35C [auth A],
D [auth B],
E [auth C],
F [auth D]
184Reston ebolavirus - RestonMutation(s): 0 
Gene Names: REBOVgp2VP35
UniProt
Find proteins for Q8JPY0 (Reston ebolavirus (strain Reston-89))
Explore Q8JPY0 
Go to UniProtKB:  Q8JPY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JPY0
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A)-3'A [auth E]18N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*UP*CP*CP*UP*CP*CP*CP*UP*CP*CP*CP*UP*CP*CP*UP*UP*CP*U)-3'B [auth F]18N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.685α = 90
b = 85.685β = 90
c = 108.812γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
XPREPdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Advisory, Refinement description