6YA2 | pdb_00006ya2

Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated)

• PDB DOI: https://doi.org/10.2210/pdb6YA2/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Orthotospovirus tomatomaculae
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

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: gel filtration

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: 67.55 kDa 
• Atom Count: 4,438 
• Modeled Residue Count: 551 
• Deposited Residue Count: 597 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein	A, B, C	199	Orthotospovirus tomatomaculae	Mutation(s): 1  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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth B], H [auth C], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.66	α = 90
b = 76.01	β = 106.56
c = 71.18	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: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary