6Y9L

Crystal structure of TSWV glycoprotein N ectodomain (sGn)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.278 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of tomato spotted wilt virus G N reveals a dimer complex formation and evolutionary link to animal-infecting viruses.

Bahat, Y., Alter, J., Dessau, M.

(2020) Proc Natl Acad Sci U S A 117: 26237-26244

  • DOI: 10.1073/pnas.2004657117
  • Primary Citation of Related Structures:  
    6Y9M, 6Y9L

  • PubMed Abstract: 

    • Tospoviridae is a family of enveloped RNA plant viruses that infect many field crops, inflicting a heavy global economic burden. These tripartite, single-stranded, negative-sense RNA viruses are transmitted from plant to plant by thrips as t ...

    Tospoviridae is a family of enveloped RNA plant viruses that infect many field crops, inflicting a heavy global economic burden. These tripartite, single-stranded, negative-sense RNA viruses are transmitted from plant to plant by thrips as the insect vector. The medium (M) segment of the viral genome encodes two envelope glycoproteins, G N and G C , which together form the envelope spikes. G C is considered the virus fusogen, while the accompanying G N protein serves as an attachment protein that binds to a yet unknown receptor, mediating the virus acquisition by the thrips carrier. Here we present the crystal structure of glycoprotein N (G N ) from the tomato spotted wilt virus (TSWV), a representative member of the Tospoviridae family. The structure suggests that G N is organized as dimers on TSWV's outer shell. Our structural data also suggest that this dimerization is required for maintaining G N structural integrity. Although the structure of the TSWV G N is different from other bunyavirus G N proteins, they all share similar domain connectivity that resembles glycoproteins from unrelated animal-infecting viruses, suggesting a common ancestor for these accompanying proteins.

    Organizational Affiliation: 

    Azrieli Faculty of Medicine, Bar-Ilan University, Safed , Israel 1311502 moshe.dessau@biu.ac.il.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GlycoproteinA, B, C, D288Tomato spotted wilt tospovirusMutation(s): 0 
Gene Names: Gn, Gc, GP
Find proteins for O55647 (Tomato spotted wilt virus)
Explore O55647 
Go to UniProtKB:  O55647
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, J
3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, I, K
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.278 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.992α = 90
b = 215.878β = 90
c = 146.368γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
AutoSolphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2020-03-09 
  • Released Date: 2020-09-30 
    • Deposition Author(s): Dessau, M., Bahat, Y.

Revision History 

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-21
    Changes: Database references
  • Version 1.2: 2020-10-28
    Changes: Database references