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- PDB-8jr3: Crystal structure of Hendra Virus attachment(G) glycoprotein muta... -

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Basic information

Entry
Database: PDB / ID: 8jr3
TitleCrystal structure of Hendra Virus attachment(G) glycoprotein mutant S586N in complex with neutralizing antibody 14F8
Components
  • Glycoprotein G
  • Heavy chain of neutralizing antibody 14F8
  • Light chain of neutralizing antibody 14F8
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Hendra virus / Nipah virus / Attachment protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHendra virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsLi, Y.H. / Huang, X.Y. / Xu, J.J. / Chen, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200762 China
CitationJournal: To Be Published
Title: Crystal structure of Hendra Virus attachment (G) glycoprotein mutant S586N in complex with neutralizing antibody 14F8
Authors: Li, Y.H. / Huang, X.Y. / Xu, J.J. / Chen, W.
History
DepositionJun 16, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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Assembly

Deposited unit
E: Glycoprotein G
F: Glycoprotein G
A: Heavy chain of neutralizing antibody 14F8
D: Light chain of neutralizing antibody 14F8
B: Heavy chain of neutralizing antibody 14F8
C: Light chain of neutralizing antibody 14F8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,27216
Polymers186,3226
Non-polymers4,95010
Water00
1
E: Glycoprotein G
B: Heavy chain of neutralizing antibody 14F8
C: Light chain of neutralizing antibody 14F8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9008
Polymers93,1613
Non-polymers2,7395
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint5 kcal/mol
Surface area36460 Å2
MethodPISA
2
F: Glycoprotein G
A: Heavy chain of neutralizing antibody 14F8
D: Light chain of neutralizing antibody 14F8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3728
Polymers93,1613
Non-polymers2,2115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-2 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.843, 257.014, 193.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules EF

#1: Protein Glycoprotein G


Mass: 46807.141 Da / Num. of mol.: 2 / Mutation: S586N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus (isolate Horse/Autralia/Hendra/1994)
Gene: G / Production host: Homo sapiens (human) / References: UniProt: O89343

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Antibody , 2 types, 4 molecules ABDC

#2: Antibody Heavy chain of neutralizing antibody 14F8


Mass: 23066.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Light chain of neutralizing antibody 14F8


Mass: 23286.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Sugars , 5 types, 10 molecules

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


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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-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
#7: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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: 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

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Details

Has ligand of interestY
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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG3350 13.5%, 100mM pH 4.7 NaAC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.22→37.79 Å / Num. obs: 44694 / % possible obs: 98.99 % / Redundancy: 5.1 % / CC1/2: 0.977 / Net I/σ(I): 6.57
Reflection shellResolution: 3.23→3.29 Å / Num. unique obs: 44663 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.22→37.79 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 2000 4.48 %
Rwork0.2155 --
obs0.2167 44670 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.22→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13086 0 328 0 13414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813727
X-RAY DIFFRACTIONf_angle_d1.41318694
X-RAY DIFFRACTIONf_dihedral_angle_d14.9125013
X-RAY DIFFRACTIONf_chiral_restr0.1372195
X-RAY DIFFRACTIONf_plane_restr0.0152348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.30.34981250.3082681X-RAY DIFFRACTION88
3.3-3.390.31521420.28123023X-RAY DIFFRACTION99
3.39-3.490.30531420.28363029X-RAY DIFFRACTION99
3.49-3.60.28781420.26483030X-RAY DIFFRACTION99
3.6-3.730.28951430.25633051X-RAY DIFFRACTION100
3.73-3.880.24481430.2353035X-RAY DIFFRACTION100
3.88-4.050.27681430.22193052X-RAY DIFFRACTION100
4.05-4.270.25711440.20563077X-RAY DIFFRACTION100
4.27-4.530.22721440.18093067X-RAY DIFFRACTION100
4.53-4.880.18451430.16853065X-RAY DIFFRACTION100
4.88-5.370.21291450.17293099X-RAY DIFFRACTION100
5.37-6.150.21061460.19893094X-RAY DIFFRACTION100
6.15-7.730.22751470.21863144X-RAY DIFFRACTION100
7.74-100.19861510.19863223X-RAY DIFFRACTION99

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