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- PDB-9cqd: Antibody 2B11 bound to the central conserved domain of RSV G -

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Basic information

Entry
Database: PDB / ID: 9cqd
TitleAntibody 2B11 bound to the central conserved domain of RSV G
Components
  • Fab 2B11 Heavy Chain
  • Fab 2B11 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 speciesRespiratory syncytial virus A2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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: Maria G Juarez / Sara M O'Rourke / John V Dzimianski / Delia Gagnon / Gabriel Penunuri / Vitor H B Serrão / Russell B Corbett-Detig / Lawrence M Kauvar / Rebecca M DuBois /
Abstract: Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in infants and older adults. The attachment glycoprotein (RSV G) binds to the chemokine receptor CX3CR1 ...Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in infants and older adults. The attachment glycoprotein (RSV G) binds to the chemokine receptor CX3CR1 to promote viral entry and modulate host immunity. Antibodies against RSV G are a known correlate of protection. Previously, several broadly reactive, high-affinity anti-RSV G human monoclonal antibodies were isolated from RSV-exposed individuals and were shown to be protective in vitro and in vivo. Here, we determined the structures of three of these antibodies in complex with RSV G and defined distinct conformational epitopes comprised of highly conserved RSV G residues. Binding competition and structural studies demonstrated that this highly conserved region displays two non-overlapping antigenic sites. Analyses of anti-RSV G antibody sequences reveal that antigenic site flexibility may promote the elicitation of diverse antibody germlines. Together, these findings provide a foundation for next-generation RSV prophylactics, and they expand concepts in vaccine design for the elicitation of germline lineage-diverse, broadly reactive, high-affinity antibodies.
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
M: Mature secreted glycoprotein G
N: Mature secreted glycoprotein G
S: Mature secreted glycoprotein G
T: Mature secreted glycoprotein G
U: Mature secreted glycoprotein G
V: Mature secreted glycoprotein G
j: Mature secreted glycoprotein G
A: Mature secreted glycoprotein G
B: Fab 2B11 Heavy Chain
F: Fab 2B11 Light Chain
G: Fab 2B11 Light Chain
I: Fab 2B11 Light Chain
J: Fab 2B11 Heavy Chain
K: Fab 2B11 Light Chain
L: Fab 2B11 Heavy Chain
O: Fab 2B11 Light Chain
P: Fab 2B11 Heavy Chain
Q: Fab 2B11 Light Chain
R: Fab 2B11 Heavy Chain
W: Fab 2B11 Light Chain
X: Fab 2B11 Heavy Chain
Y: Fab 2B11 Light Chain
Z: Fab 2B11 Heavy Chain
H: Fab 2B11 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)452,60224
Polymers452,60224
Non-polymers00
Water00
1
M: Mature secreted glycoprotein G
W: Fab 2B11 Light Chain
X: Fab 2B11 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)56,5753
Polymers56,5753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-38 kcal/mol
Surface area19820 Å2
MethodPISA
2
N: Mature secreted glycoprotein G
Q: Fab 2B11 Light Chain
R: Fab 2B11 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)56,5753
Polymers56,5753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-37 kcal/mol
Surface area20370 Å2
MethodPISA
3
S: Mature secreted glycoprotein G
O: Fab 2B11 Light Chain
P: Fab 2B11 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)56,5753
Polymers56,5753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-39 kcal/mol
Surface area19680 Å2
MethodPISA
4
T: Mature secreted glycoprotein G
B: Fab 2B11 Heavy Chain
F: Fab 2B11 Light Chain


Theoretical massNumber of molelcules
Total (without water)56,5753
Polymers56,5753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-37 kcal/mol
Surface area20160 Å2
MethodPISA
5
U: Mature secreted glycoprotein G
K: Fab 2B11 Light Chain
L: Fab 2B11 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)56,5753
Polymers56,5753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-39 kcal/mol
Surface area20390 Å2
MethodPISA
6
V: Mature secreted glycoprotein G
Y: Fab 2B11 Light Chain
Z: Fab 2B11 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)56,5753
Polymers56,5753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-39 kcal/mol
Surface area19870 Å2
MethodPISA
7
j: Mature secreted glycoprotein G
I: Fab 2B11 Light Chain
J: Fab 2B11 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)56,5753
Polymers56,5753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-40 kcal/mol
Surface area20110 Å2
MethodPISA
8
A: Mature secreted glycoprotein G
G: Fab 2B11 Light Chain
H: Fab 2B11 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)56,5753
Polymers56,5753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-27 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.654, 184.339, 161.236
Angle α, β, γ (deg.)90.000, 96.880, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide
Mature secreted glycoprotein G / Mature sG


Mass: 5735.633 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03423
#2: Antibody
Fab 2B11 Heavy Chain


Mass: 27321.760 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody
Fab 2B11 Light Chain


Mass: 23517.857 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 0.22M Ammonium Citrate Dibasic and 15% 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: Nov 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.1→92.17 Å / Num. obs: 78391 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 67.15 Å2 / CC1/2: 0.984 / Net I/σ(I): 3.3
Reflection shellResolution: 3.1→3.15 Å / Num. unique obs: 3862 / CC1/2: 0.348

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→80.04 Å / SU ML: 0.647 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.2419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3242 2048 2.64 %
Rwork0.2919 75631 -
obs0.2927 77679 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.5 Å2
Refinement stepCycle: LAST / Resolution: 3.1→80.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25773 0 0 0 25773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626371
X-RAY DIFFRACTIONf_angle_d0.877835865
X-RAY DIFFRACTIONf_chiral_restr0.05874103
X-RAY DIFFRACTIONf_plane_restr0.00714572
X-RAY DIFFRACTIONf_dihedral_angle_d14.51079424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.170.4211180.39014480X-RAY DIFFRACTION88.83
3.17-3.250.38921580.36615104X-RAY DIFFRACTION99.94
3.25-3.340.35671460.34665012X-RAY DIFFRACTION100
3.34-3.440.35091260.33185108X-RAY DIFFRACTION100
3.44-3.550.36321390.32385083X-RAY DIFFRACTION99.96
3.55-3.680.38161290.33775056X-RAY DIFFRACTION99.71
3.68-3.820.40111460.36015020X-RAY DIFFRACTION99.4
3.82-40.35641450.32975030X-RAY DIFFRACTION99.62
4-4.210.34031290.29645079X-RAY DIFFRACTION99.66
4.21-4.470.28211350.2675108X-RAY DIFFRACTION99.68
4.47-4.820.31671330.24425056X-RAY DIFFRACTION99.81
4.82-5.30.30561400.25195109X-RAY DIFFRACTION99.75
5.3-6.070.32431230.2755093X-RAY DIFFRACTION99.9
6.07-7.640.30971360.28295131X-RAY DIFFRACTION99.94
7.64-80.040.24631450.24235162X-RAY DIFFRACTION99.92

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