1H2D

Ebola virus matrix protein VP40 N-terminal domain in complex with RNA (Low-resolution VP40[31-212] variant).

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.306 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The Matrix Protein Vp40 from Ebola Virus Octamerizes Into Pore-Like Structures with Specific RNA Binding Properties

Gomis-Ruth, F.X., Dessen, A., Timmins, J., Bracher, A., Kolesnikowa, L., Becker, S., Klenk, H.D., Weissenhorn, W.

(2003) Structure 11: 423

  • DOI: 10.1016/s0969-2126(03)00050-9
  • Primary Citation of Related Structures:  
    1H2D, 1H2C

  • PubMed Abstract: 

    • The Ebola virus membrane-associated matrix protein VP40 is thought to be crucial for assembly and budding of virus particles. Here we present the crystal structure of a disk-shaped octameric form of VP40 formed by four antiparallel homodimers of the ...

    The Ebola virus membrane-associated matrix protein VP40 is thought to be crucial for assembly and budding of virus particles. Here we present the crystal structure of a disk-shaped octameric form of VP40 formed by four antiparallel homodimers of the N-terminal domain. The octamer binds an RNA triribonucleotide containing the sequence 5'-U-G-A-3' through its inner pore surface, and its oligomerization and RNA binding properties are facilitated by two conformational changes when compared to monomeric VP40. The selective RNA interaction stabilizes the ring structure and confers in vitro SDS resistance to octameric VP40. SDS-resistant octameric VP40 is also found in Ebola virus-infected cells, which suggests that VP40 has an additional function in the life cycle of the virus besides promoting virus assembly and budding off the plasma membrane.

    Related Citations: 
    • Crystal Structure of the Matrix Protein Vp40 from Ebola Virus
      Dessen, A., Volchkov, V., Dolnik, O., Klenk, H.D., Weissenhorn, W.
      (2000) EMBO J 19: 4228
    Organizational Affiliation: 

    European Molecular Biology Laboratory (EMBL), 6 rue Jules Horowitz, 38042, Grenoble, France.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MATRIX PROTEIN VP40A, B182Ebola virus sp.Mutation(s): 0 
Find proteins for Q05128 (Zaire ebolavirus (strain Mayinga-76))
Explore Q05128 
Go to UniProtKB:  Q05128
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*UP*GP*AP)-3'R, S3Escherichia coli
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CL
    Query on CL
    Download Ideal Coordinates CCD File 
    A, B
    		CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.329 
    • R-Value Work: 0.305 
    • R-Value Observed: 0.306 
    • Space Group: P 62 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 79.61α = 90
    b = 79.61β = 90
    c = 239.18γ = 120
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    SCALAdata scaling
    BEASTphasing
    AMoREphasing
    REFMACrefinement

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2003-04-10
      Type: Initial release
    • Version 1.1: 2011-05-08
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2019-05-08
      Changes: Data collection, Experimental preparation, Other