4DWA

Crystal structure of an active-site mutant of the glycoprotein Erns from the pestivirus BVDV-1 in complex with a CpUpC trinucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of the Pestivirus Envelope Glycoprotein E(rns) and Mechanistic Analysis of Its Ribonuclease Activity.

Krey, T.Bontems, F.Vonrhein, C.Vaney, M.C.Bricogne, G.Rumenapf, T.Rey, F.A.

(2012) Structure 20: 862-873

  • DOI: 10.1016/j.str.2012.03.018
  • Primary Citation of Related Structures:  
    4DVK, 4DVL, 4DVN, 4DW3, 4DW4, 4DW5, 4DW7, 4DWA, 4DWC

  • PubMed Abstract: 
  • Pestiviruses, which belong to the Flaviviridae family of RNA viruses, are important agents of veterinary diseases causing substantial economical losses in animal farming worldwide. Pestivirus particles display three envelope glycoproteins at their surface: E(rns), E1, and E2 ...

    Pestiviruses, which belong to the Flaviviridae family of RNA viruses, are important agents of veterinary diseases causing substantial economical losses in animal farming worldwide. Pestivirus particles display three envelope glycoproteins at their surface: E(rns), E1, and E2. We report here the crystal structure of the catalytic domain of E(rns), the ribonucleolytic activity of which is believed to counteract the innate immunity of the host. The structure reveals a three-dimensional fold corresponding to T2 ribonucleases from plants and fungi. Cocrystallization experiments with mono- and oligonucleotides revealed the structural basis for substrate recognition at two binding sites previously identified for T2 RNases. A detailed analysis of poly-U cleavage products using (31)P-NMR and size exclusion chromatography, together with molecular docking studies, provides a comprehensive mechanistic picture of E(rns) activity on its substrates and reveals the presence of at least one additional nucleotide binding site.


    Organizational Affiliation

    Unité de Virologie Structurale, Institut Pasteur, 75015 Paris, France. tkrey@pasteur.fr



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E(rns) glycoproteinA, B167Bovine viral diarrhea virus 1-CP7Mutation(s): 1 
Gene Names: Erns
EC: 3.4.22 (UniProt), 3.4.21.113 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q96662 (Bovine viral diarrhea virus (strain CP7))
Explore Q96662 
Go to UniProtKB:  Q96662
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*CP*UP*C)-3')C [auth D]3N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Oligosaccharides

    Help

    Entity ID: 3
    MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
    beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]5N-Glycosylation Oligosaccharides Interaction
    Glycosylation Resources
    GlyTouCan:  G68945PX
    GlyCosmos:  G68945PX
    GlyGen:  G68945PX
    Entity ID: 4
    MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
    2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, H2N-Glycosylation Oligosaccharides Interaction
    Glycosylation Resources
    GlyTouCan:  G42666HT
    GlyCosmos:  G42666HT
    GlyGen:  G42666HT
    Entity ID: 5
    MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
    beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG6N-Glycosylation Oligosaccharides Interaction
    Glycosylation Resources
    GlyTouCan:  G02534MS
    GlyCosmos:  G02534MS
    GlyGen:  G02534MS
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.01 Å
    • R-Value Free: 0.236 
    • R-Value Work: 0.195 
    • R-Value Observed: 0.197 
    • Space Group: P 65 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 105.213α = 90
    b = 105.213β = 90
    c = 210.904γ = 120
    Software Package:
    Software NamePurpose
    SCALAdata scaling
    PHASERphasing
    BUSTER-TNTrefinement
    PDB_EXTRACTdata extraction
    XDSdata scaling
    XDSdata reduction
    BUSTERrefinement

    Structure Validation

    View Full Validation Report



    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2012-05-23
      Type: Initial release
    • Version 2.0: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary