6YA2

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.244
R-Value Work: 0.213
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 67.55 kDa
Atom Count: 4,438
Modelled Residue Count: 551
Deposited Residue Count: 597
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36291
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C]	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		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.244
R-Value Work: 0.213
R-Value Observed: 0.214
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

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Ligand Structure Quality Assessment

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: Data collection, Database references, Refinement description

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Deposit Data

Help and Resources

6YA2

Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)