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- PDB-7te1: SARS-CoV-2 Receptor Binding Domain in Complex with Ab17 -

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Basic information

Entry
Database: PDB / ID: 7te1
TitleSARS-CoV-2 Receptor Binding Domain in Complex with Ab17
Components
  • Ab17 heavy chain
  • Ab17 light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM/Viral Protein / antibody-antigen complex / SARS-CoV-2 / receptor binding domain / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsHauser, B.M. / Schmidt, A.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI146779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F30 AI160908 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007753 United States
CitationJournal: Cell Rep / Year: 2022
Title: Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting.
Authors: Blake M Hauser / Maya Sangesland / Kerri J St Denis / Evan C Lam / James Brett Case / Ian W Windsor / Jared Feldman / Timothy M Caradonna / Ty Kannegieter / Michael S Diamond / Alejandro B ...Authors: Blake M Hauser / Maya Sangesland / Kerri J St Denis / Evan C Lam / James Brett Case / Ian W Windsor / Jared Feldman / Timothy M Caradonna / Ty Kannegieter / Michael S Diamond / Alejandro B Balazs / Daniel Lingwood / Aaron G Schmidt /
Abstract: Eliciting antibodies to surface-exposed viral glycoproteins can generate protective responses that control and prevent future infections. Targeting conserved sites may reduce the likelihood of viral ...Eliciting antibodies to surface-exposed viral glycoproteins can generate protective responses that control and prevent future infections. Targeting conserved sites may reduce the likelihood of viral escape and limit the spread of related viruses with pandemic potential. Here we leverage rational immunogen design to focus humoral responses on conserved epitopes. Using glycan engineering and epitope scaffolding in boosting immunogens, we focus murine serum antibody responses to conserved receptor binding motif (RBM) and receptor binding domain (RBD) epitopes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike imprinting. Although all engineered immunogens elicit a robust SARS-CoV-2-neutralizing serum response, RBM-focusing immunogens exhibit increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV; structural characterization of representative antibodies defines a conserved epitope. RBM-focused sera confer protection against SARS-CoV-2 challenge. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses without compromising SARS-CoV-2 protection. These engineering strategies are adaptable to other viral glycoproteins for targeting conserved epitopes.
History
DepositionJan 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Ab17 heavy chain
F: Ab17 light chain
H: Ab17 heavy chain
L: Ab17 light chain
D: Spike protein S1
E: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)142,2236
Polymers142,2236
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance, Biolayer interferometry was performed to determine the binding kinetics of the Ab17 Fab to the SARS-CoV-2 receptor binding domain.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.931, 207.931, 86.662
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Antibody Ab17 heavy chain


Mass: 23975.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293-F / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human)
#2: Antibody Ab17 light chain


Mass: 23363.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 23771.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S, 2 / Cell line (production host): HEK 293S GntI -/- / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0 and 30% v/v Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.5→79.99 Å / Num. obs: 24539 / % possible obs: 99.98 % / Redundancy: 21.1 % / Biso Wilson estimate: 104.62 Å2 / Rmerge(I) obs: 0.395 / Rpim(I) all: 0.088 / Rrim(I) all: 0.405 / Net I/σ(I): 10.1
Reflection shellResolution: 3.5→3.55 Å / Num. unique obs: 4607 / CC1/2: 0.235 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASERphasing
XDSdata reduction
PDB_EXTRACT3.27data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J, 4L5F, 4HCl

6m0j

4l5f

4hcl


Resolution: 3.5→79.99 Å / SU ML: 0.5915 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.5634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3442 1206 4.91 %
Rwork0.2965 23332 -
obs0.2989 24538 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.58 Å2
Refinement stepCycle: LAST / Resolution: 3.5→79.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9099 0 0 0 9099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319323
X-RAY DIFFRACTIONf_angle_d0.801512673
X-RAY DIFFRACTIONf_chiral_restr0.04911397
X-RAY DIFFRACTIONf_plane_restr0.00511611
X-RAY DIFFRACTIONf_dihedral_angle_d5.08481264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.640.40321320.33962551X-RAY DIFFRACTION100
3.64-3.810.37551300.30952526X-RAY DIFFRACTION100
3.81-4.010.37971320.31762547X-RAY DIFFRACTION100
4.01-4.260.3321330.28352563X-RAY DIFFRACTION100
4.26-4.590.33811320.26072570X-RAY DIFFRACTION100
4.59-5.050.30981330.25352566X-RAY DIFFRACTION100
5.05-5.780.31261350.27782622X-RAY DIFFRACTION100
5.78-7.280.34571360.33612620X-RAY DIFFRACTION100
7.28-79.990.35591430.31112767X-RAY DIFFRACTION99.93

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