6Y9M | pdb_00006y9m

Crystal structure of TSWV glycoprotein N ectodomain (sGn)

• PDB DOI: https://doi.org/10.2210/pdb6Y9M/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Tomato spotted wilt virus (strain Brazilian BR-01)
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-03-10 Released: 2020-09-30 
• Deposition Author(s): Dessau, M., Bahat, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.261 (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: cross-linking, mass spectrometry

Biological Assembly 2  

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

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

Biological Assembly Evidence: mass spectrometry, cross-linking

Macromolecule Content 

• Total Structure Weight: 130.96 kDa 
• Atom Count: 6,441 
• Modeled Residue Count: 791 
• Deposited Residue Count: 1,136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein	A, B, C, D	284	Tomato spotted wilt virus (strain Brazilian BR-01)	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, H, I, K, L	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	3		N/A
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	Q [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	M [auth A], N [auth A], O [auth B], P [auth B], R [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.2	α = 90
b = 218.2	β = 90
c = 145.5	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: 2020-10-21
  Changes: Database references
• Version 1.2: 2020-10-28
  Changes: Database references
• Version 1.3: 2021-04-14
  Changes: Database references
• Version 1.4: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary