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- PDB-6y9l: Crystal structure of TSWV glycoprotein N ectodomain (sGn) -

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Basic information

Entry
Database: PDB / ID: 6y9l
TitleCrystal structure of TSWV glycoprotein N ectodomain (sGn)
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / Envelope protein / attachment / viral entry / receptor binding / viral assembly
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / host cell Golgi membrane / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein precursor/M polyprotein precursor, Tospovirus type / Bunyavirus glycoprotein G1 / Bunyavirus glycoprotein G1
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesTomato spotted wilt virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4.1 Å
AuthorsDessau, M. / Bahat, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Crystal structure of tomato spotted wilt virus G N reveals a dimer complex formation and evolutionary link to animal-infecting viruses
Authors: Bahat, Y. / Alter, J. / Dessau, M.
History
DepositionMar 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 14, 2021Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Glycoprotein
D: Glycoprotein
A: Glycoprotein
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,38012
Polymers128,7024
Non-polymers3,6788
Water00
1
B: Glycoprotein
D: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3736
Polymers64,3512
Non-polymers2,0224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint9 kcal/mol
Surface area24170 Å2
MethodPISA
2
A: Glycoprotein
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0076
Polymers64,3512
Non-polymers1,6574
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint7 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.992, 215.878, 146.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Glycoprotein


Mass: 32175.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato spotted wilt virus / Gene: Gn, Gc / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A3G1GK10, UniProt: O55647*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.26 Å3/Da / Density % sol: 76.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium sulfate 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 4.1→49.02 Å / Num. obs: 20685 / % possible obs: 98.8 % / Redundancy: 6.442 % / Biso Wilson estimate: 227.343 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.114 / Χ2: 1.043 / Net I/σ(I): 8.39 / Num. measured all: 133260 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
4.1-4.215.8713.8770.417562150812880.2744.23785.4
4.21-4.336.7323.2510.5710098150015000.3893.526100
4.33-4.456.4852.0220.939416145414520.5492.19899.9
4.45-4.596.8971.4831.319684140414040.8741.604100
4.59-4.746.8331.1121.89389137813740.8271.20499.7
4.74-4.916.7540.7952.528854131113110.9160.862100
4.91-5.096.7630.6443.138528126212610.9360.69999.9
5.09-5.36.5390.5333.668115124212410.9350.5899.9
5.3-5.536.3630.4464.167617119711970.9480.486100
5.53-5.86.6380.365.317415111711170.9610.391100
5.8-6.126.4990.2597.047038108310830.9760.281100
6.12-6.496.7540.1959.576977103310330.9850.211100
6.49-6.946.6210.13312.9163569609600.9920.145100
6.94-7.496.3330.09717.1556818978970.9950.106100
7.49-8.215.7980.06921.7948418358350.9960.076100
8.21-9.185.8650.05227.9844637627610.9980.05799.9
9.18-10.66.1620.04729.8741846796790.9980.051100
10.6-12.985.7980.04530.4733515785780.9980.049100
12.98-18.365.2360.04529.8624194624620.9980.05100
18.36-49.025.0480.04729.4912722732520.9980.05292.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: MIRAS / Resolution: 4.1→49.02 Å / SU ML: 0.83 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 40.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3019 1028 5 %
Rwork0.277 19527 -
obs0.2784 20555 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 853.6 Å2 / Biso mean: 331.0241 Å2 / Biso min: 206.15 Å2
Refinement stepCycle: final / Resolution: 4.1→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 243 0 6325
Biso mean--432.87 --
Num. residues----783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.1-4.320.44041340.42251590
4.32-4.590.41371470.374278899
4.59-4.950.31441450.2949276699
4.95-5.440.35111490.2818281799
5.44-6.230.30991480.28592828100
6.23-7.840.33051500.30892847100

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