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- PDB-6y9m: Crystal structure of TSWV glycoprotein N ectodomain (sGn) -

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Basic information

Entry
Database: PDB / ID: 6y9m
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
PHOSPHATE ION / Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesTomato spotted wilt virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 10, 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 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)130,96418
Polymers126,5274
Non-polymers4,43714
Water1267
1
A: Glycoprotein
D: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1518
Polymers63,2642
Non-polymers1,8886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-3 kcal/mol
Surface area23100 Å2
MethodPISA
2
B: Glycoprotein
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,81310
Polymers63,2642
Non-polymers2,5498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-23 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.200, 218.200, 145.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycoprotein


Mass: 31631.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato spotted wilt virus (strain Brazilian BR-01)
Gene: Gn, Gc / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A3G1GK10, UniProt: P36291*PLUS

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Sugars , 3 types, 8 molecules

#2: 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.: 6
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
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 13 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: PO4
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.3 Å3/Da / Density % sol: 76.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 4000 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.03961 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03961 Å / Relative weight: 1
ReflectionResolution: 3.4→49.16 Å / Num. obs: 36920 / % possible obs: 99.7 % / Redundancy: 39.604 % / Biso Wilson estimate: 158.007 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.145 / Χ2: 1.003 / Net I/σ(I): 20.04 / Num. measured all: 1462177 / Scaling rejects: 2250
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
3.4-3.4529.6577.8160.645761157715430.4327.95197.8
3.45-3.541.9566.270.9361465147314650.5536.34699.5
3.5-3.5541.8235.4041.157758138413810.615.46999.8
3.55-3.641.5174.5311.3854802132513200.714.58699.6
3.6-3.740.7923.6681.6799656245024430.7773.71499.7
3.7-3.840.132.7022.2286761216621620.8022.73699.8
3.8-437.6721.7833.34140744374237360.9081.80799.8
4-4.541.6770.6629.46279321670567020.9910.67100
4.5-540.6730.25722.07175831432443230.9980.26100
5-5.538.8540.18727.83112598290028980.9980.1999.9
5.5-641.9990.15233.585174202820280.9990.154100
6-740.3420.10444.38101300251125110.9990.105100
7-835.4180.07255.9650966144014390.9990.07399.9
8-940.1070.05871.913405184984910.059100
9-1038.9650.05573.872240557557510.056100
10-2035.20.05571.56474151352134710.05599.6
20-49.1631.1570.05767.8561692171980.9990.05891.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y9L

6y9l


Resolution: 3.4→49.16 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 1840 4.99 %
Rwork0.2593 35004 -
obs0.2605 36844 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 370.12 Å2 / Biso mean: 159.3377 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.4→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6148 0 286 7 6441
Biso mean--237.59 113.08 -
Num. residues----791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.490.41831260.42252617274398
3.49-3.590.42451370.37926542791100
3.59-3.710.39571540.362326772831100
3.71-3.840.33581280.333826842812100
3.84-40.34771410.317426532794100
4-4.180.29521240.27427142838100
4.18-4.40.27171360.243326562792100
4.4-4.670.21461540.216626812835100
4.67-5.030.23081240.202527082832100
5.04-5.540.29071650.234426962861100
5.54-6.340.26511420.269627132855100
6.34-7.980.29611540.264127312885100
7.99-49.160.27251550.24822820297599
Refinement TLS params.Method: refined / Origin x: 136.5262 Å / Origin y: 67.1446 Å / Origin z: 54.6466 Å
111213212223313233
T0.9248 Å2-0.2282 Å20.1294 Å2-0.9359 Å2-0.0072 Å2--1.0064 Å2
L0.065 °2-0.5582 °2-0.0678 °2-0.3435 °20.3004 °2--0.5952 °2
S0.1689 Å °0.0459 Å °-0.0015 Å °-0.0117 Å °-0.116 Å °-0.0182 Å °-0.1283 Å °-0.1089 Å °0.1609 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA110 - 304
2X-RAY DIFFRACTION1allA501 - 512
3X-RAY DIFFRACTION1allB110 - 310
4X-RAY DIFFRACTION1allB501 - 510
5X-RAY DIFFRACTION1allC108 - 303
6X-RAY DIFFRACTION1allC501 - 512
7X-RAY DIFFRACTION1allD110 - 308
8X-RAY DIFFRACTION1allD501 - 504
9X-RAY DIFFRACTION1allS1 - 8

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