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- PDB-6ya2: Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated) -

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Basic information

Entry
Database: PDB / ID: 6ya2
TitleCrystal structure of TSWV glycoprotein N ectodomain (Trypsin treated)
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 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 1.3Nov 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5539
Polymers65,8203
Non-polymers1,7346
Water1,42379
1
A: Glycoprotein
B: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1716
Polymers43,8802
Non-polymers1,2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-4 kcal/mol
Surface area21030 Å2
MethodPISA
2
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3823
Polymers21,9401
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint5 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.660, 76.010, 71.180
Angle α, β, γ (deg.)90.000, 106.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycoprotein


Mass: 21939.869 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: This construct is a S214C mutant construct based on 6YA0 entry.
Source: (gene. exp.) Tomato spotted wilt virus / Gene: Gn, Gc / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A3G1GK10, UniProt: O55647*PLUS
#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.: 2 / Source method: isolated from a natural 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: 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.: 4 / Source method: isolated from a natural 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% PEG 8,000 (w/v) 0.1 M tris pH 7.5 0.2 M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→18.85 Å / Num. obs: 24477 / % possible obs: 98.5 % / Redundancy: 6.976 % / Biso Wilson estimate: 67.877 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.108 / Χ2: 1.026 / Net I/σ(I): 13.14 / Num. measured all: 170741 / Scaling rejects: 32
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
2.5-2.67.121.833119225275027000.561.97798.2
2.6-2.77.1551.3271.4416800235923480.7031.43199.5
2.7-2.87.0780.9372.1114290202320190.8221.01199.8
2.8-2.97.1250.7192.7212455175417480.870.77599.7
2.9-36.8570.5313.6210389152615150.9140.57599.3
3-3.56.6490.1978.5734434529851790.990.21497.8
3.5-47.2850.09318.1921717299629810.9970.199.5
4-57.0550.0530.1820877297129590.9990.05499.6
5-76.5220.04931.9612561200819260.9980.05395.9
7-107.4710.03245.7556037527500.9990.03499.7
10-137.2570.03151.316112212220.9990.033100
13-156.750.03249.6345969680.9990.03598.6
15-18.855.1610.0440.11320128620.9990.04448.4

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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: 6YA0

6ya0


Resolution: 2.5→18.85 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1026 5.03 %
Rwork0.2129 19391 -
obs0.2145 20417 82.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.65 Å2 / Biso mean: 75.2674 Å2 / Biso min: 16.24 Å2
Refinement stepCycle: final / Resolution: 2.5→18.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 112 79 4438
Biso mean--143.49 57.06 -
Num. residues----551
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.630.3138590.2948109032
2.63-2.80.26171170.2975211564
2.8-3.010.37931520.2997294489
3.01-3.320.2991700.2515323897
3.32-3.790.24491760.21263334100
3.79-4.760.21991760.18223343100
Refinement TLS params.Method: refined / Origin x: -13.7352 Å / Origin y: -8.7137 Å / Origin z: 4.6998 Å
111213212223313233
T0.1986 Å20.022 Å2-0.0601 Å2-0.1594 Å2-0.0227 Å2--0.2165 Å2
L1.89 °20.2947 °20.0571 °2-1.076 °2-0.0304 °2--0.9243 °2
S0.0484 Å °-0.2075 Å °-0.1774 Å °0.0766 Å °-0.0214 Å °-0.0601 Å °-0.0012 Å °-0.0402 Å °-0.012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA109 - 296
2X-RAY DIFFRACTION1allA297 - 301
3X-RAY DIFFRACTION1allB107 - 296
4X-RAY DIFFRACTION1allB301 - 303
5X-RAY DIFFRACTION1allC110 - 295
6X-RAY DIFFRACTION1allC296 - 301
7X-RAY DIFFRACTION1allZ1 - 122

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