6YA0

Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated)

• PDB DOI: https://doi.org/10.2210/pdb6YA0/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Orthotospovirus tomatomaculae
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-03-11 Released: 2020-09-30 
• Deposition Author(s): Dessau, M., Bahat, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.261 
• R-Value Work: 0.217 
• R-Value Observed: 0.222 

Starting Model: experimental

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

• DOI: https://doi.org/10.1073/pnas.2004657117

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.09 kDa 
• Atom Count: 4,396 
• Modelled Residue Count: 553 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein	A, B, C	288	Orthotospovirus tomatomaculae	Mutation(s): 0  Gene Names: Gn, Gc
UniProt
Find proteins for P36291 (Tomato spotted wilt virus (strain Brazilian Br-01)) Explore P36291  Go to UniProtKB:  P36291
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G90333CG GlyCosmos:  G90333CG GlyGen:  G90333CG

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], H [auth B], I [auth B], J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACT	G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NH4	K [auth C]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.261 
• R-Value Work: 0.217 
• R-Value Observed: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.82	α = 90
b = 74.85	β = 103.27
c = 81.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• 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: 2021-04-14
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary