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- PDB-8el2: SARS-CoV-2 RBD bound to neutralizing antibody Fab ICO-hu23 -

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Basic information

Entry
Database: PDB / ID: 8el2
TitleSARS-CoV-2 RBD bound to neutralizing antibody Fab ICO-hu23
Components
  • (Fab ICO-hu23 ...) x 2
  • Spike protein S1
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / Fab / SARS-CoV-2 / receptor-binding domain / neutralizing antibody / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsBesaw, J.E. / Kuo, A. / Morizumi, T. / Ernst, O.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06862 Canada
CitationJournal: PLoS Pathog / Year: 2023
Title: Broadly neutralizing humanized SARS-CoV-2 antibody binds to a conserved epitope on Spike and provides antiviral protection through inhalation-based delivery in non-human primates.
Authors: Paule Hermet / Benoît Delache / Cecile Herate / Esther Wolf / Gaily Kivi / Erkki Juronen / Karl Mumm / Eva Žusinaite / Denis Kainov / Eve Sankovski / Kai Virumäe / Anu Planken / Andres ...Authors: Paule Hermet / Benoît Delache / Cecile Herate / Esther Wolf / Gaily Kivi / Erkki Juronen / Karl Mumm / Eva Žusinaite / Denis Kainov / Eve Sankovski / Kai Virumäe / Anu Planken / Andres Merits / Jessica E Besaw / Ai Woon Yee / Takefumi Morizumi / Kyumhyuk Kim / Anling Kuo / Asma Berriche / Nathalie Dereuddre-Bosquet / Quentin Sconosciuti / Thibaut Naninck / Francis Relouzat / Mariangela Cavarelli / Mart Ustav / Derek Wilson / Oliver P Ernst / Andres Männik / Roger LeGrand / Mart Ustav /
Abstract: The COVID-19 pandemic represents a global challenge that has impacted and is expected to continue to impact the lives and health of people across the world for the foreseeable future. The rollout of ...The COVID-19 pandemic represents a global challenge that has impacted and is expected to continue to impact the lives and health of people across the world for the foreseeable future. The rollout of vaccines has provided highly anticipated relief, but effective therapeutics are required to further reduce the risk and severity of infections. Monoclonal antibodies have been shown to be effective as therapeutics for SARS-CoV-2, but as new variants of concern (VoC) continue to emerge, their utility and use have waned due to limited or no efficacy against these variants. Furthermore, cumbersome systemic administration limits easy and broad access to such drugs. As well, concentrations of systemically administered antibodies in the mucosal epithelium, a primary site of initial infection, are dependent on neonatal Fc receptor mediated transport and require high drug concentrations. To reduce the viral load more effectively in the lung, we developed an inhalable formulation of a SARS-CoV-2 neutralizing antibody binding to a conserved epitope on the Spike protein, ensuring pan-neutralizing properties. Administration of this antibody via a vibrating mesh nebulization device retained antibody integrity and resulted in effective distribution of the antibody in the upper and lower respiratory tract of non-human primates (NHP). In comparison with intravenous administration, significantly higher antibody concentrations can be obtained in the lung, resulting in highly effective reduction in viral load post SARS-CoV-2 challenge. This approach may reduce the barriers of access and uptake of antibody therapeutics in real-world clinical settings and provide a more effective blueprint for targeting existing and potentially emerging respiratory tract viruses.
History
DepositionSep 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab ICO-hu23 Heavy Chain
L: Fab ICO-hu23 Light Chain
I: Fab ICO-hu23 Heavy Chain
K: Fab ICO-hu23 Light Chain
A: Spike protein S1
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,54012
Polymers148,7826
Non-polymers7576
Water00
1
H: Fab ICO-hu23 Heavy Chain
L: Fab ICO-hu23 Light Chain
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7706
Polymers74,3913
Non-polymers3793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Fab ICO-hu23 Heavy Chain
K: Fab ICO-hu23 Light Chain
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7706
Polymers74,3913
Non-polymers3793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.300, 140.300, 202.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-519-

HIS

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSILEILE(chain 'A' and (resid 336 through 358 or resid 361...AE336 - 35820 - 42
121CYSCYSTYRTYR(chain 'A' and (resid 336 through 358 or resid 361...AE361 - 36945 - 53
131ALAALAPHEPHE(chain 'A' and (resid 336 through 358 or resid 361...AE372 - 37756 - 61
141CYSCYSPROPRO(chain 'A' and (resid 336 through 358 or resid 361...AE379 - 38463 - 68
151LYSLYSVALVAL(chain 'A' and (resid 336 through 358 or resid 361...AE386 - 40770 - 91
161GLNGLNARGARG(chain 'A' and (resid 336 through 358 or resid 361...AE409 - 45793 - 141
171ASNASNLEULEU(chain 'A' and (resid 336 through 358 or resid 361...AE460 - 461144 - 145
181PROPROALAALA(chain 'A' and (resid 336 through 358 or resid 361...AE463 - 475147 - 159
191THRTHRGLUGLU(chain 'A' and (resid 336 through 358 or resid 361...AE478 - 516162 - 200
1101LEULEULEULEU(chain 'A' and (resid 336 through 358 or resid 361...AE518202
1111CYSCYSCYSCYS(chain 'A' and (resid 336 through 358 or resid 361...AE525209
2121CYSCYSILEILE(chain 'B' and (resid 336 through 369 or resid 372...BF336 - 35820 - 42
2131CYSCYSTYRTYR(chain 'B' and (resid 336 through 369 or resid 372...BF361 - 36945 - 53
2141ALAALAPHEPHE(chain 'B' and (resid 336 through 369 or resid 372...BF372 - 37756 - 61
2151CYSCYSPROPRO(chain 'B' and (resid 336 through 369 or resid 372...BF379 - 38463 - 68
2161LYSLYSVALVAL(chain 'B' and (resid 336 through 369 or resid 372...BF386 - 40770 - 91
2171GLNGLNARGARG(chain 'B' and (resid 336 through 369 or resid 372...BF409 - 45793 - 141
2181ASNASNLEULEU(chain 'B' and (resid 336 through 369 or resid 372...BF460 - 461144 - 145
2191PROPROALAALA(chain 'B' and (resid 336 through 369 or resid 372...BF463 - 475147 - 159
2201THRTHRGLUGLU(chain 'B' and (resid 336 through 369 or resid 372...BF478 - 516162 - 200
2211LEULEULEULEU(chain 'B' and (resid 336 through 369 or resid 372...BF518202
2221CYSCYSCYSCYS(chain 'B' and (resid 336 through 369 or resid 372...BF525209
1232GLUGLUSERSER(chain 'H' and (resid 1 through 195 or resid 197...HA1 - 1371 - 137
1242GLYGLYSERSER(chain 'H' and (resid 1 through 195 or resid 197...HA143 - 195143 - 195
1252SERSERTHRTHR(chain 'H' and (resid 1 through 195 or resid 197...HA197 - 214197 - 214
1262VALVALVALVAL(chain 'H' and (resid 1 through 195 or resid 197...HA216 - 220216 - 220
1272PROPROLYSLYS(chain 'H' and (resid 1 through 195 or resid 197...HA222 - 223222 - 223
2282GLUGLUSERSER(chain 'I' and (resid 1 through 195 or resid 197...IC1 - 1371 - 137
2292GLYGLYSERSER(chain 'I' and (resid 1 through 195 or resid 197...IC143 - 195143 - 195
2302SERSERTHRTHR(chain 'I' and (resid 1 through 195 or resid 197...IC197 - 214197 - 214
2312VALVALVALVAL(chain 'I' and (resid 1 through 195 or resid 197...IC216 - 220216 - 220
2322PROPROLYSLYS(chain 'I' and (resid 1 through 195 or resid 197...IC222 - 223222 - 223
1333SERSERPROPRO(chain 'K' and (resid 1 through 113 or resid 115 through 213))KD1 - 1131 - 113
1343ALAALATHRTHR(chain 'K' and (resid 1 through 113 or resid 115 through 213))KD115 - 213115 - 213
2353SERSERPROPRO(chain 'L' and (resid 1 through 113 or resid 115...LB1 - 1131 - 113
2363ALAALATHRTHR(chain 'L' and (resid 1 through 113 or resid 115...LB115 - 213115 - 213

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules HILK

#1: Antibody Fab ICO-hu23 Heavy Chain


Mass: 25479.584 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 Fab ICO-hu23 Light Chain


Mass: 22802.115 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)

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Protein / Sugars , 2 types, 4 molecules AB

#3: Protein Spike protein S1


Mass: 26109.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 4 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10% PEG 8000, 0.1 M MES at pH 5.5, 0.2 M zinc acetate, 3% ethylene glycol, 3% glycerol, 10 mM cadmium chloride hydrate, 4% v/v polypropylene glycol P 400, 3% v/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.89→46.78 Å / Num. obs: 52265 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 78.8 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.7
Reflection shellResolution: 2.89→2.98 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4458 / CC1/2: 0.317 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7beh

7beh


Resolution: 2.89→46.78 Å / SU ML: 0.5885 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.6703
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2815 3859 3.88 %
Rwork0.2387 95661 -
obs0.2404 51233 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.02 Å2
Refinement stepCycle: LAST / Resolution: 2.89→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9488 0 42 0 9530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00589801
X-RAY DIFFRACTIONf_angle_d1.025413369
X-RAY DIFFRACTIONf_chiral_restr0.05941476
X-RAY DIFFRACTIONf_plane_restr0.00521703
X-RAY DIFFRACTIONf_dihedral_angle_d21.26613483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.930.5341250.4143136X-RAY DIFFRACTION89.71
2.93-2.960.40961380.39583405X-RAY DIFFRACTION99.83
2.96-30.42871350.3973437X-RAY DIFFRACTION99.86
3-3.040.41471350.38273486X-RAY DIFFRACTION100
3.04-3.090.38651320.36213366X-RAY DIFFRACTION99.91
3.09-3.130.41381350.34483432X-RAY DIFFRACTION99.94
3.13-3.180.44811460.34383429X-RAY DIFFRACTION99.97
3.18-3.230.35871420.32843400X-RAY DIFFRACTION100
3.23-3.290.40281370.3133460X-RAY DIFFRACTION99.83
3.29-3.350.32981380.31283406X-RAY DIFFRACTION99.94
3.35-3.410.37441360.29023448X-RAY DIFFRACTION99.94
3.41-3.480.29041380.27433395X-RAY DIFFRACTION99.94
3.48-3.560.26811440.26463423X-RAY DIFFRACTION100
3.56-3.640.33471340.25763469X-RAY DIFFRACTION99.83
3.64-3.730.27641400.26523412X-RAY DIFFRACTION99.97
3.73-3.830.26481340.24963416X-RAY DIFFRACTION100
3.83-3.950.27661340.24333423X-RAY DIFFRACTION100
3.95-4.070.25971440.22233460X-RAY DIFFRACTION100
4.07-4.220.23831340.21253424X-RAY DIFFRACTION100
4.22-4.390.24261400.19173429X-RAY DIFFRACTION99.97
4.39-4.590.23791360.19263422X-RAY DIFFRACTION99.83
4.59-4.830.25251440.18933428X-RAY DIFFRACTION99.78
4.83-5.130.26311340.19353423X-RAY DIFFRACTION99.97
5.13-5.530.19451370.1993413X-RAY DIFFRACTION99.75
5.53-6.080.22411420.19923452X-RAY DIFFRACTION99.97
6.08-6.960.24511500.22193400X-RAY DIFFRACTION100
6.96-8.760.26981260.21443458X-RAY DIFFRACTION99.94
8.76-46.780.30791490.24063409X-RAY DIFFRACTION99.75

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