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- PDB-8jr5: Crystal structure of Hendra Virus attachment(G) glycoprotein muta... -

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Basic information

Entry
Database: PDB / ID: 8jr5
TitleCrystal structure of Hendra Virus attachment(G) glycoprotein mutant S586N
ComponentsGlycoprotein G
KeywordsVIRAL PROTEIN / Hendra virus / Nipah virus / attachment glycoprotein
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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
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 16, 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
A: Glycoprotein G
B: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9247
Polymers93,6142
Non-polymers1,3095
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.926, 63.658, 121.622
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: Henipavirus hendraense / References: UniProt: O89343
#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.: 1 / Source method: obtained synthetically
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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG3350 14%, 10mM MgCl2, 5mM NiCL2, PIPES 6.5

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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 S 9M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 19331 / % possible obs: 98.52 % / Redundancy: 6.2 % / CC1/2: 0.98 / Net I/σ(I): 12.68
Reflection shellResolution: 3.3→3.418 Å / Num. unique obs: 19216 / CC1/2: 0.98

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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: 3.3→41.59 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 961 5 %
Rwork0.2583 --
obs0.2599 19231 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6369 0 84 0 6453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126604
X-RAY DIFFRACTIONf_angle_d1.5898988
X-RAY DIFFRACTIONf_dihedral_angle_d14.412416
X-RAY DIFFRACTIONf_chiral_restr0.0861031
X-RAY DIFFRACTIONf_plane_restr0.011140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.470.35021270.34292459X-RAY DIFFRACTION94
3.47-3.690.38841370.34282568X-RAY DIFFRACTION98
3.69-3.970.34681380.29152613X-RAY DIFFRACTION99
3.97-4.370.2731370.23082615X-RAY DIFFRACTION100
4.37-50.19051380.192638X-RAY DIFFRACTION100
5.01-6.30.27561410.24682670X-RAY DIFFRACTION100
6.3-100.30021430.26332707X-RAY DIFFRACTION99

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