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- PDB-8yxi: Crystal structure of SFTSV Gn in complex with a neutralizing anti... -

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Basic information

Entry
Database: PDB / ID: 8yxi
TitleCrystal structure of SFTSV Gn in complex with a neutralizing antibody 40C10
Components
  • Envelopment polyprotein
  • heavy chain
  • light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / neutralizing antibody / SFTSV / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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
Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesSevere fever with thrombocytopenia syndrome virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsYang, P. / Guo, Y. / Zhang, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271256 China
CitationJournal: Plos Pathog. / Year: 2024
Title: Molecular mechanism and structure-guided humanization of a broadly neutralizing antibody against SFTSV.
Authors: Yang, P. / Wu, X. / Shang, H. / Sun, Z. / Wang, Z. / Song, Z. / Yuan, H. / Deng, F. / Shen, S. / Guo, Y. / Zhang, N.
History
DepositionApr 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: heavy chain
B: light chain
A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8485
Polymers85,8373
Non-polymers1,0112
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-10 kcal/mol
Surface area31570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.753, 65.906, 73.738
Angle α, β, γ (deg.)90.00, 105.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules CB

#1: Antibody heavy chain


Mass: 23827.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody light chain


Mass: 23511.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein / Non-polymers , 2 types, 356 molecules A

#3: Protein Envelopment polyprotein / M polyprotein


Mass: 38497.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe fever with thrombocytopenia syndrome virus
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2Z4HIM0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#5: 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: 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

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Details

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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.04 M Citric acid, 0.06 M BIS-TRIS propane/pH 6.4, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→94.37 Å / Num. obs: 35578 / % possible obs: 99.8 % / Redundancy: 1.9 % / CC1/2: 0.94 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.9
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.9 / Num. unique obs: 2622 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→36.63 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 1695 4.77 %
Rwork0.2058 --
obs0.2078 35511 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5770 0 67 355 6192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.053
X-RAY DIFFRACTIONf_dihedral_angle_d11.313841
X-RAY DIFFRACTIONf_chiral_restr0.064893
X-RAY DIFFRACTIONf_plane_restr0.0091035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.30461490.27482785X-RAY DIFFRACTION99
2.47-2.550.30841480.27872774X-RAY DIFFRACTION99
2.55-2.640.331520.26812807X-RAY DIFFRACTION100
2.64-2.750.28921160.25842824X-RAY DIFFRACTION100
2.75-2.870.28541360.23842771X-RAY DIFFRACTION99
2.87-3.020.26511450.21872822X-RAY DIFFRACTION100
3.02-3.210.2311420.20432820X-RAY DIFFRACTION100
3.21-3.460.26291480.20192799X-RAY DIFFRACTION100
3.46-3.810.26141230.18222857X-RAY DIFFRACTION100
3.81-4.360.20731220.16782843X-RAY DIFFRACTION99
4.36-5.490.20451480.17122846X-RAY DIFFRACTION100
5.49-36.630.22431660.20532868X-RAY DIFFRACTION99

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