6YA0 | pdb_00006ya0

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 (Depositor), 0.259 (DCC)
R-Value Work:
0.217 (Depositor), 0.217 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 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

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36291
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

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 J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.261 (Depositor), 0.259 (DCC)
R-Value Work: 0.217 (Depositor), 0.217 (DCC)
R-Value Observed: 0.222 (Depositor)

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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-09-30

Deposition Author(s):

Dessau, M.

Bahat, Y.

Revision History (Full details and data files)

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