Macromolecule Content

Total Structure Weight: 98.09 kDa
Atom Count: 4396
Residue Count: 553
Unique protein chains: 1

6YA0

Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated)

DOI: 10.2210/pdb6YA0/pdb

Classification: VIRAL PROTEIN
Organism(s): Tomato spotted wilt tospovirus
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

wwPDB Validation 3D Report Full Report

Literature

First structure of a glycoprotein from enveloped plant virus

Bahat, Y., Alter, J., Dessau, M.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein	A, B, C	288	Tomato spotted wilt tospovirus	Mutation(s): 0 Gene Names: Gn, Gc, GP
Find proteins for O55647 (Tomato spotted wilt virus) Explore O55647 Go to UniProtKB: O55647
Protein Feature View Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Oligosaccharides Interaction

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [A] SDF format, chain H [B] SDF format, chain I [B] SDF format, chain J [C] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain H [B] MOL2 format, chain I [B] MOL2 format, chain J [C]	A, B, C	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [B] MOL2 format, chain G [B]	B	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain K [C] MOL2 format, chain K [C]	C	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Ligand Interaction

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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2020-03-11
Released Date: 2020-09-30

Deposition Author(s):

Revision History

Version 1.0: 2020-09-30
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.