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- PDB-6ya0: Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated) -

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Basic information

Entry
Database: PDB / ID: 6ya0
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


modulation by virus of host process / host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / 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
ACETATE ION / AMMONIUM ION / Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesTomato spotted wilt virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,09311
Polymers96,5263
Non-polymers1,5668
Water57632
1
A: Glycoprotein
B: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2957
Polymers64,3512
Non-polymers9445
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-5 kcal/mol
Surface area20500 Å2
MethodPISA
2
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7984
Polymers32,1751
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint8 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.820, 74.850, 81.280
Angle α, β, γ (deg.)90.000, 103.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glycoprotein


Mass: 32175.436 Da / Num. of mol.: 3
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

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Sugars , 2 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}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.: 5
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

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Non-polymers , 3 types, 34 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28% PEG 3350 (w/v) 0.1 M tris pH 7.5 2% Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.86→49.91 Å / Num. obs: 18724 / % possible obs: 99.6 % / Redundancy: 3.414 % / Biso Wilson estimate: 93.781 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.076 / Χ2: 1.031 / Net I/σ(I): 10.5 / Num. measured all: 63929 / Scaling rejects: 8
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
2.86-2.933.5621.6350.884991140314010.4371.92699.9
2.93-3.013.51.2391.174718135213480.581.46599.7
3.01-3.13.4880.7121.834520130012960.8490.84499.7
3.1-3.23.3930.4642.544194123912360.9260.55199.8
3.2-3.33.1990.3273.383948124112340.9530.39499.4
3.3-3.423.3180.2384.413972119611970.9760.285100
3.42-3.553.560.1856.044069114611430.9820.21899.7
3.55-3.693.5240.1317.283905111011080.9930.15599.8
3.69-3.863.4750.1138.763701107010650.9920.13499.5
3.86-4.043.4750.07611.893562102910250.9960.0999.6
4.04-4.263.2970.06313.6631989739700.9960.07599.7
4.26-4.523.2210.05117.0828768968930.9960.06299.7
4.52-4.833.5650.04620.6630878678660.9970.05499.9
4.83-5.223.5070.04521.4828278118060.9970.05399.4
5.22-5.723.4410.04820.9625537477420.9960.05799.3
5.72-6.43.1690.04621.1521176716680.9960.05699.6
6.4-7.383.3150.03824.4620026056040.9980.04599.8
7.38-9.043.4350.03229.9917215045010.9980.03899.4
9.04-12.793.1230.0330.5812404023970.9980.03698.8
12.79-49.913.250.03131.457282302240.9980.03797.4

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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: 6Y9M

6y9m


Resolution: 2.86→49.91 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.34 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 1425 10 %
Rwork0.2175 12818 -
obs0.2219 14243 75.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.37 Å2 / Biso mean: 91.9214 Å2 / Biso min: 24.95 Å2
Refinement stepCycle: final / Resolution: 2.86→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 9 32 4305
Biso mean--57.81 63.45 -
Num. residues----553
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.86-2.960.4635210.312219412
2.96-3.080.3922700.301961937
3.08-3.220.2661990.265690254
3.22-3.390.34481320.2609119070
3.39-3.60.28621630.23146187
3.6-3.880.26081850.2401166699
3.88-4.270.23861870.1991685100
4.27-4.890.21711880.16451684100
4.89-6.160.2611860.21931685100
Refinement TLS params.Method: refined / Origin x: -16.6058 Å / Origin y: 2.7064 Å / Origin z: -9.8881 Å
111213212223313233
T0.4048 Å2-0.0541 Å2-0.0074 Å2-0.3486 Å2-0.0797 Å2--0.2396 Å2
L3.2031 °2-1.5148 °20.1831 °2-2.6204 °2-0.4115 °2--1.3748 °2
S-0.0229 Å °0.3751 Å °-0.0384 Å °-0.2255 Å °0.0909 Å °0.058 Å °-0.151 Å °-0.1545 Å °-0.0151 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA107 - 500
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allB108 - 500
4X-RAY DIFFRACTION1allC112 - 500
5X-RAY DIFFRACTION1allE1 - 38
6X-RAY DIFFRACTION1allD1

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