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- PDB-9cqb: Antibody 1G8 bound to the central conserved domain of RSV G -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9cqb
TitleAntibody 1G8 bound to the central conserved domain of RSV G
Components
  • Fab 1G8 Heavy Chain
  • Fab 1G8 Light Chain
  • Mature secreted glycoprotein G
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / respiratory syncytial virus / G glycoprotein / 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 / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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
Similarity search - Domain/homology
Major surface glycoprotein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJuarez, M.J. / DuBois, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI166066 United States
CitationJournal: Sci Rep / Year: 2025
Title: Structures of respiratory syncytial virus G bound to broadly reactive antibodies provide insights into vaccine design.
Authors: Juarez, M.G. / O'Rourke, S.M. / Dzimianski, J.V. / Gagnon, D. / Penunuri, G. / Serrao, V.H.B. / Corbett-Detig, R.B. / Kauvar, L.M. / DuBois, R.M.
History
DepositionJul 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab 1G8 Light Chain
B: Fab 1G8 Heavy Chain
D: Mature secreted glycoprotein G


Theoretical massNumber of molelcules
Total (without water)57,2753
Polymers57,2753
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-44 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.394, 67.394, 286.346
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 Fab 1G8 Light Chain


Mass: 23567.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 1G8 Heavy Chain


Mass: 27972.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Mature secreted glycoprotein G / Mature sG


Mass: 5735.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03423
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: .15M Sodium Thiocyanate and 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→286.35 Å / Num. obs: 27297 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 51.91 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 1310 / CC1/2: 0.553

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→58.37 Å / SU ML: 0.4537 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.1111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2632 2007 7.38 %
Rwork0.2258 25188 -
obs0.2286 27195 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 0 16 3594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873666
X-RAY DIFFRACTIONf_angle_d1.09054995
X-RAY DIFFRACTIONf_chiral_restr0.0591567
X-RAY DIFFRACTIONf_plane_restr0.0084636
X-RAY DIFFRACTIONf_dihedral_angle_d16.711312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.41981370.36991734X-RAY DIFFRACTION99.68
2.56-2.630.38241360.35061760X-RAY DIFFRACTION99.58
2.63-2.710.33531430.3241773X-RAY DIFFRACTION99.84
2.71-2.80.35571400.32331769X-RAY DIFFRACTION99.74
2.8-2.90.32551380.29761747X-RAY DIFFRACTION99.95
2.9-3.010.35341420.28911774X-RAY DIFFRACTION99.84
3.01-3.150.30871420.26611770X-RAY DIFFRACTION99.95
3.15-3.320.29881420.25731783X-RAY DIFFRACTION100
3.32-3.520.31141420.23651792X-RAY DIFFRACTION100
3.52-3.80.27711440.22961807X-RAY DIFFRACTION100
3.8-4.180.23421450.20481821X-RAY DIFFRACTION100
4.18-4.780.19871440.16891817X-RAY DIFFRACTION100
4.78-6.020.18821470.17861860X-RAY DIFFRACTION100
6.02-58.370.23051650.18261981X-RAY DIFFRACTION100

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