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- PDB-7t8w: Structure of antibody 3G12 bound to Respiratory Syncytial Virus G... -

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Basic information

Entry
Database: PDB / ID: 7t8w
TitleStructure of antibody 3G12 bound to Respiratory Syncytial Virus G central conserved domain mutant S177Q
Components
  • 3G12 Fab Heavy chain
  • 3G12 Fab Light chain
  • Mature secreted glycoprotein G
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Respiratory syncytial virus / human antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Translation of respiratory syncytial virus mRNAs / adhesion receptor-mediated virion attachment to host cell / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / plasma membrane
Similarity search - Function
Major surface glycoprotein G / Pneumovirus attachment glycoprotein G / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major surface glycoprotein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Human respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsNunez Castrejon, A.M. / O'Rourke, S.M. / Kauvar, L.M. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56AI141537 United States
CitationJournal: J.Virol. / Year: 2022
Title: Structure-Based Design and Antigenic Validation of Respiratory Syncytial Virus G Immunogens.
Authors: Nunez Castrejon, A.M. / O'Rourke, S.M. / Kauvar, L.M. / DuBois, R.M.
History
DepositionDec 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: 3G12 Fab Light chain
H: 3G12 Fab Heavy chain
D: Mature secreted glycoprotein G


Theoretical massNumber of molelcules
Total (without water)53,8343
Polymers53,8343
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-34 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.391, 139.391, 98.045
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Antibody 3G12 Fab Light chain


Mass: 23218.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody 3G12 Fab Heavy chain


Mass: 24838.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide Mature secreted glycoprotein G / Mature sG


Mass: 5776.684 Da / Num. of mol.: 1 / Mutation: S177Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Strain: A2 / Production host: Escherichia coli (E. coli) / Strain (production host): T7Express / References: UniProt: P03423
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: 5.11 Å3/Da / Density % sol: 75.92 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 1.8 M ammonium sulfate, 100 mM sodium acetate trihydrate pH 4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→98.05 Å / Num. obs: 20300 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 57.29 Å2 / CC1/2: 0.974 / Rpim(I) all: 0.164 / Rsym value: 0.164 / Χ2: 0.97 / Net I/σ(I): 5.8
Reflection shellResolution: 3.1→3.31 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3613 / CC1/2: 0.567 / Χ2: 0.93 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UVO

6uvo


Resolution: 3.1→76.11 Å / SU ML: 0.4027 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 2006 9.89 %
Rwork0.2369 18268 -
obs0.2382 20274 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.35 Å2
Refinement stepCycle: LAST / Resolution: 3.1→76.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 0 0 3598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413690
X-RAY DIFFRACTIONf_angle_d2.02595032
X-RAY DIFFRACTIONf_chiral_restr0.1086566
X-RAY DIFFRACTIONf_plane_restr0.0092644
X-RAY DIFFRACTIONf_dihedral_angle_d14.37571308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.38551410.34581295X-RAY DIFFRACTION100
3.18-3.260.30391410.32181274X-RAY DIFFRACTION100
3.26-3.360.34411400.29931266X-RAY DIFFRACTION100
3.36-3.470.31391470.29831298X-RAY DIFFRACTION100
3.47-3.590.31671390.27531282X-RAY DIFFRACTION100
3.59-3.740.26351420.26391297X-RAY DIFFRACTION100
3.74-3.910.25261450.24891296X-RAY DIFFRACTION100
3.91-4.110.24541450.22771295X-RAY DIFFRACTION100
4.11-4.370.20841460.20971303X-RAY DIFFRACTION100
4.37-4.710.2081450.19511303X-RAY DIFFRACTION100
4.71-5.180.2011400.18481321X-RAY DIFFRACTION100
5.18-5.930.22481400.21771302X-RAY DIFFRACTION100
5.93-7.470.25571430.24181345X-RAY DIFFRACTION100
7.47-76.110.20841520.20081391X-RAY DIFFRACTION99.87

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