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- PDB-8wsq: A protective human antibody against respiratory syncytial virus b... -

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Basic information

Entry
Database: PDB / ID: 8wsq
TitleA protective human antibody against respiratory syncytial virus by targeting a prefusion epitope across sites IV and V of the viral fusion glycoprotein.
Components
  • Fusion glycoprotein F0
  • RV11-H scFv
  • RV11-L scFv
KeywordsANTIVIRAL PROTEIN/VIRAL PROTEIN / RSV monoclonal antibody / RSV fusion glycoprotein / IV and V epitope / RSV prophylaxis / ANTIVIRAL PROTEIN-VIRAL PROTEIN complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesRespiratory syncytial virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXu, S.Y. / Chai, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A protective human antibody against respiratory syncytial virus by targeting a prefusion epitope across sites IV and V of the viral fusion glycoprotein.
Authors: Xu, S.Y. / Chai, Y.
History
DepositionOct 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Fusion glycoprotein F0
A: RV11-H scFv
B: RV11-L scFv


Theoretical massNumber of molelcules
Total (without water)80,8773
Polymers80,8773
Non-polymers00
Water00
1
F: Fusion glycoprotein F0
A: RV11-H scFv
B: RV11-L scFv

F: Fusion glycoprotein F0
A: RV11-H scFv
B: RV11-L scFv

F: Fusion glycoprotein F0
A: RV11-H scFv
B: RV11-L scFv


Theoretical massNumber of molelcules
Total (without water)242,6329
Polymers242,6329
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)183.656, 183.656, 183.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Fusion glycoprotein F0


Mass: 52296.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus / Production host: Homo sapiens (human) / References: UniProt: C3UPB8
#2: Antibody RV11-H scFv


Mass: 14823.241 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody RV11-L scFv


Mass: 13757.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 291 K / Method: counter-diffusion
Details: 0.15 M DL-Malic acid pH 6.2, 0.1 M Imidazole pH 7.0, 27% (v/v) polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→49.08 Å / Num. obs: 22923 / % possible obs: 100 % / Redundancy: 38.7 % / Biso Wilson estimate: 51.64 Å2 / CC1/2: 0.9 / Net I/σ(I): 16.7
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 2243 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.08 Å / SU ML: 0.3918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.28 1125 4.99 %
Rwork0.2472 21420 -
obs0.2488 22545 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.27 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 0 0 0 5228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335322
X-RAY DIFFRACTIONf_angle_d0.71617221
X-RAY DIFFRACTIONf_chiral_restr0.0489833
X-RAY DIFFRACTIONf_plane_restr0.0049920
X-RAY DIFFRACTIONf_dihedral_angle_d13.48791933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.38341530.37052623X-RAY DIFFRACTION98.3
3.03-3.190.40051630.33132635X-RAY DIFFRACTION98.8
3.19-3.390.36121540.30422670X-RAY DIFFRACTION98.78
3.4-3.650.32531130.29172687X-RAY DIFFRACTION98.8
3.66-4.020.32431300.25122633X-RAY DIFFRACTION96.88
4.02-4.60.24991420.21132643X-RAY DIFFRACTION97.48
4.61-5.80.21361160.19732730X-RAY DIFFRACTION98.79
5.8-49.080.20531540.20632799X-RAY DIFFRACTION99.23

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