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- PDB-9cqa: Structure of antibody 1G1 bound to the central conserved region o... -

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Basic information

Entry
Database: PDB / ID: 9cqa
TitleStructure of antibody 1G1 bound to the central conserved region of RSV G
Components
  • Fab 1G1 Heavy Chain
  • Fab1G1 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: 1.74 Å
AuthorsJuarez, M.G. / DuBois, R.M.
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
E: Fab 1G1 Heavy Chain
F: Fab1G1 Light Chain
D: Fab 1G1 Heavy Chain
G: Fab1G1 Light Chain
A: Mature secreted glycoprotein G
B: Mature secreted glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,10010
Polymers114,7166
Non-polymers3844
Water7,080393
1
E: Fab 1G1 Heavy Chain
F: Fab1G1 Light Chain
A: Mature secreted glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5505
Polymers57,3583
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-71 kcal/mol
Surface area21410 Å2
MethodPISA
2
D: Fab 1G1 Heavy Chain
G: Fab1G1 Light Chain
B: Mature secreted glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5505
Polymers57,3583
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-44 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.418, 80.753, 175.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab 1G1 Heavy Chain


Mass: 28290.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab1G1 Light Chain


Mass: 23331.760 Da / Num. of mol.: 2
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.: 2
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS (pH 6.5), 0.2M Ammonium Sulfate, and 24.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 1.74→47.32 Å / Num. obs: 110905 / % possible obs: 99.2 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 1.74→1.77 Å / Num. unique obs: 5008 / CC1/2: 0.457

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: 000)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→47.32 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 2004 1.81 %
Rwork0.2108 --
obs0.2111 110700 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7038 0 20 393 7451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077236
X-RAY DIFFRACTIONf_angle_d0.9699874
X-RAY DIFFRACTIONf_dihedral_angle_d14.0232542
X-RAY DIFFRACTIONf_chiral_restr0.0631108
X-RAY DIFFRACTIONf_plane_restr0.0111258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.32471290.34487148X-RAY DIFFRACTION93
1.78-1.830.30591420.30357673X-RAY DIFFRACTION99
1.83-1.890.26311470.26697782X-RAY DIFFRACTION100
1.89-1.950.26831300.24967709X-RAY DIFFRACTION100
1.95-2.020.29441480.24337766X-RAY DIFFRACTION99
2.02-2.10.25631470.22627715X-RAY DIFFRACTION100
2.1-2.190.23141440.21447737X-RAY DIFFRACTION99
2.19-2.310.25681340.22077770X-RAY DIFFRACTION100
2.31-2.450.24881540.21717790X-RAY DIFFRACTION100
2.45-2.640.22631310.21947839X-RAY DIFFRACTION100
2.64-2.910.22931590.21737785X-RAY DIFFRACTION99
2.91-3.330.20741430.20917858X-RAY DIFFRACTION99
3.33-4.190.21151440.18797945X-RAY DIFFRACTION100
4.19-47.320.19441520.18868179X-RAY DIFFRACTION99

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