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- PDB-8zhz: Structure of Ikoma lyssavirus glycoprotein in pre-fusion state -

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Basic information

Entry
Database: PDB / ID: 8zhz
TitleStructure of Ikoma lyssavirus glycoprotein in pre-fusion state
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / Glycoprotein / Ikoma lyssavirus / membrane fusion / VIRUS
Function / homologyRhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain / viral envelope / virion membrane / membrane / Glycoprotein
Function and homology information
Biological speciesIkoma lyssavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsLu, G.W. / Yang, F.L. / Lin, S. / Yang, J. / Ye, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Ikoma lyssavirus glycoprotein in pre-fusion state
Authors: Lu, G.W. / Yang, F.L. / Lin, S. / Yang, J. / Ye, F.
History
DepositionMay 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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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
E: Glycoprotein
F: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,05416
Polymers300,2326
Non-polymers2,82210
Water00
1
A: Glycoprotein
B: Glycoprotein
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,4258
Polymers150,1163
Non-polymers1,3095
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint3 kcal/mol
Surface area54740 Å2
MethodPISA
2
D: Glycoprotein
E: Glycoprotein
F: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6298
Polymers150,1163
Non-polymers1,5125
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint5 kcal/mol
Surface area54510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.915, 90.746, 151.311
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycoprotein


Mass: 50038.707 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ikoma lyssavirus / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: J7JVS8
#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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.: 7 / Source method: obtained synthetically / 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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2M Ammonium phosphate dibasic (pH 8.3), 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 74555 / % possible obs: 99.6 % / Redundancy: 5.1 % / CC1/2: 0.969 / Net I/σ(I): 9.15
Reflection shellHighest resolution: 2.88 Å / Num. unique obs: 7419 / CC1/2: 0.659

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→46.64 Å / SU ML: 0.41 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2812 3613 4.86 %
Rwork0.2251 --
obs0.2278 74334 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17726 0 182 0 17908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01118326
X-RAY DIFFRACTIONf_angle_d1.34824739
X-RAY DIFFRACTIONf_dihedral_angle_d7.7142456
X-RAY DIFFRACTIONf_chiral_restr0.0682686
X-RAY DIFFRACTIONf_plane_restr0.0123166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.920.3803800.32092133X-RAY DIFFRACTION76
2.92-2.960.38471350.29392676X-RAY DIFFRACTION99
2.96-30.3691530.27782716X-RAY DIFFRACTION99
3-3.050.34821300.28252730X-RAY DIFFRACTION99
3.05-3.10.36841710.29042676X-RAY DIFFRACTION99
3.1-3.150.32171450.29572727X-RAY DIFFRACTION99
3.15-3.20.32521570.27822676X-RAY DIFFRACTION99
3.2-3.260.33541530.25892736X-RAY DIFFRACTION99
3.26-3.320.27581200.24972774X-RAY DIFFRACTION99
3.32-3.390.35741510.24142682X-RAY DIFFRACTION99
3.39-3.460.27341350.23712758X-RAY DIFFRACTION99
3.46-3.540.27681540.23172717X-RAY DIFFRACTION99
3.54-3.630.33151540.23812740X-RAY DIFFRACTION99
3.63-3.730.31981360.24012711X-RAY DIFFRACTION99
3.73-3.840.26561060.22082797X-RAY DIFFRACTION100
3.84-3.960.29511400.20972732X-RAY DIFFRACTION100
3.96-4.10.26081280.20022771X-RAY DIFFRACTION100
4.11-4.270.24971300.19572726X-RAY DIFFRACTION100
4.27-4.460.23951170.18712799X-RAY DIFFRACTION100
4.46-4.70.22741300.18732746X-RAY DIFFRACTION100
4.7-4.990.23361440.18252786X-RAY DIFFRACTION100
4.99-5.380.27721650.20422742X-RAY DIFFRACTION99
5.38-5.920.25651150.23052794X-RAY DIFFRACTION100
5.92-6.770.3161550.24692764X-RAY DIFFRACTION100
6.77-8.520.29041590.21552807X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -24.9963 Å / Origin y: -0.2865 Å / Origin z: -37.8745 Å
111213212223313233
T0.4594 Å2-0.0204 Å2-0.0021 Å2-0.3792 Å20.0249 Å2--0.3914 Å2
L0.7639 °2-0.1291 °2-0.0335 °2-0.1197 °2-0.0076 °2--0.0758 °2
S0.034 Å °0.0019 Å °-0.0044 Å °-0.014 Å °-0.0244 Å °0.0078 Å °-0.0026 Å °-0.0025 Å °-0.0136 Å °
Refinement TLS groupSelection details: all

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