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- PDB-7lud: Crystal structure of Fab ADI-14442 -

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Basic information

Entry
Database: PDB / ID: 7lud
TitleCrystal structure of Fab ADI-14442
Components
  • ADI-14442 Fab Heavy chain
  • ADI-14442 Fab Light chain
KeywordsIMMUNE SYSTEM / RSV F / Fab / Antibody / Viral fusion protein
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRush, S.A. / McLellan, J.S.
CitationJournal: Immunity / Year: 2021
Title: Vaccination with prefusion-stabilized respiratory syncytial virus fusion protein induces genetically and antigenically diverse antibody responses.
Authors: Maryam Mukhamedova / Daniel Wrapp / Chen-Hsiang Shen / Morgan S A Gilman / Tracy J Ruckwardt / Chaim A Schramm / Larissa Ault / Lauren Chang / Alexandrine Derrien-Colemyn / Sarah A M Lucas / ...Authors: Maryam Mukhamedova / Daniel Wrapp / Chen-Hsiang Shen / Morgan S A Gilman / Tracy J Ruckwardt / Chaim A Schramm / Larissa Ault / Lauren Chang / Alexandrine Derrien-Colemyn / Sarah A M Lucas / Amy Ransier / Samuel Darko / Emily Phung / Lingshu Wang / Yi Zhang / Scott A Rush / Bharat Madan / Guillaume B E Stewart-Jones / Pamela J Costner / LaSonji A Holman / Somia P Hickman / Nina M Berkowitz / Nicole A Doria-Rose / Kaitlyn M Morabito / Brandon J DeKosky / Martin R Gaudinski / Grace L Chen / Michelle C Crank / John Misasi / Nancy J Sullivan / Daniel C Douek / Peter D Kwong / Barney S Graham / Jason S McLellan / John R Mascola /
Abstract: An effective vaccine for respiratory syncytial virus (RSV) is an unrealized public health goal. A single dose of the prefusion-stabilized fusion (F) glycoprotein subunit vaccine (DS-Cav1) ...An effective vaccine for respiratory syncytial virus (RSV) is an unrealized public health goal. A single dose of the prefusion-stabilized fusion (F) glycoprotein subunit vaccine (DS-Cav1) substantially increases serum-neutralizing activity in healthy adults. We sought to determine whether DS-Cav1 vaccination induces a repertoire mirroring the pre-existing diversity from natural infection or whether antibody lineages targeting specific epitopes predominate. We evaluated RSV F-specific B cell responses before and after vaccination in six participants using complementary B cell sequencing methodologies and identified 555 clonal lineages. DS-Cav1-induced lineages recognized the prefusion conformation of F (pre-F) and were genetically diverse. Expressed antibodies recognized all six antigenic sites on the pre-F trimer. We identified 34 public clonotypes, and structural analysis of two antibodies from a predominant clonotype revealed a common mode of recognition. Thus, vaccination with DS-Cav1 generates a diverse polyclonal response targeting the antigenic sites on pre-F, supporting the development and advanced testing of pre-F-based vaccines against RSV.
History
DepositionFeb 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: ADI-14442 Fab Heavy chain
L: ADI-14442 Fab Light chain
A: ADI-14442 Fab Heavy chain
B: ADI-14442 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1978
Polymers95,8134
Non-polymers3844
Water00
1
H: ADI-14442 Fab Heavy chain
L: ADI-14442 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1955
Polymers47,9062
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-56 kcal/mol
Surface area19500 Å2
MethodPISA
2
A: ADI-14442 Fab Heavy chain
B: ADI-14442 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0033
Polymers47,9062
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-34 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.879, 158.669, 60.180
Angle α, β, γ (deg.)90.000, 104.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ADI-14442 Fab Heavy chain


Mass: 23805.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody ADI-14442 Fab Light chain


Mass: 24100.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.8 M ammonium sulfate, 0.09 M HEPES pH 7.5 and 0.05% ethyl acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→54.63 Å / Num. obs: 20217 / % possible obs: 96.9 % / Redundancy: 3.1 % / CC1/2: 0.961 / Net I/σ(I): 6
Reflection shellResolution: 2.9→3.08 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3321 / CC1/2: 0.654

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ddr

6ddr


Resolution: 2.9→50.16 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.233 --
Rwork0.194 --
obs-20193 96.75 %
Displacement parametersBiso max: 168.59 Å2 / Biso mean: 55.3416 Å2 / Biso min: 26.75 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6679 0 20 0 6699

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