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- PDB-8f0i: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 8f0i
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody COVA309-22
Components
  • COVA309-22 heavy chain
  • COVA309-22 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / SARS-CoV-2 / coronavirus / RBD / COVID-19 / IMMUNE SYSTEM / VIRAL 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 / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support Netherlands, United States, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)91818627 Netherlands
Bill & Melinda Gates FoundationINV-004923 United States
Citation
Journal: iScience / Year: 2023
Title: Broad SARS-CoV-2 neutralization by monoclonal and bispecific antibodies derived from a Gamma-infected individual.
Authors: Denise Guerra / Tim Beaumont / Laura Radić / Gius Kerster / Karlijn van der Straten / Meng Yuan / Jonathan L Torres / Wen-Hsin Lee / Hejun Liu / Meliawati Poniman / Ilja Bontjer / Judith A ...Authors: Denise Guerra / Tim Beaumont / Laura Radić / Gius Kerster / Karlijn van der Straten / Meng Yuan / Jonathan L Torres / Wen-Hsin Lee / Hejun Liu / Meliawati Poniman / Ilja Bontjer / Judith A Burger / Mathieu Claireaux / Tom G Caniels / Jonne L Snitselaar / Tom P L Bijl / Sabine Kruijer / Gabriel Ozorowski / David Gideonse / Kwinten Sliepen / Andrew B Ward / Dirk Eggink / Godelieve J de Bree / Ian A Wilson / Rogier W Sanders / Marit J van Gils /
Abstract: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has remained a medical threat due to the evolution of multiple variants that acquire resistance to vaccines and ...The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has remained a medical threat due to the evolution of multiple variants that acquire resistance to vaccines and prior infection. Therefore, it is imperative to discover monoclonal antibodies (mAbs) that neutralize a broad range of SARS-CoV-2 variants. A stabilized spike glycoprotein was used to enrich antigen-specific B cells from an individual with a primary Gamma variant infection. Five mAbs selected from those B cells showed considerable neutralizing potency against multiple variants, with COVA309-35 being the most potent against the autologous virus, as well as Omicron BA.1 and BA.2, and COVA309-22 having binding and neutralization activity against Omicron BA.4/5, BQ.1.1, and XBB.1. When combining the COVA309 mAbs as cocktails or bispecific antibodies, the breadth and potency were improved. In addition, the mechanism of cross-neutralization of the COVA309 mAbs was elucidated by structural analysis. Altogether these data indicate that a Gamma-infected individual can develop broadly neutralizing antibodies.
#1: Journal: Biorxiv / Year: 2022
Title: Broad SARS-CoV-2 Neutralization by Monoclonal and Bispecific Antibodies Derived from a Gamma-infected Individual
Authors: Guerra, D. / Beaumont, T. / Radic, L. / Kerster, G. / van der Straten, K. / Yuan, M. / Torres, J. / Lee, W.H. / Liu, H. / Poniman, M. / Bontjer, I. / Burger, J.A. / Claireaux, M. / Caniels, ...Authors: Guerra, D. / Beaumont, T. / Radic, L. / Kerster, G. / van der Straten, K. / Yuan, M. / Torres, J. / Lee, W.H. / Liu, H. / Poniman, M. / Bontjer, I. / Burger, J.A. / Claireaux, M. / Caniels, T.G. / Snitselaar, J.L. / Bijl, T.P.L. / Kruijer, S. / Ozorowski, G. / Gideonse, D. / Sliepen, K. / Ward, A.B. / Eggink, D. / de Bree, G.J. / Wilson, I.A. / Sanders, R.W. / van Gils, M.J.
History
DepositionNov 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
C: COVA309-22 heavy chain
D: COVA309-22 light chain
B: Spike protein S1
E: COVA309-22 heavy chain
F: COVA309-22 light chain
G: Spike protein S1
H: COVA309-22 heavy chain
I: COVA309-22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,44212
Polymers211,7789
Non-polymers6643
Water00
1
A: Spike protein S1
C: COVA309-22 heavy chain
D: COVA309-22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8144
Polymers70,5933
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-32 kcal/mol
Surface area28470 Å2
MethodPISA
2
B: Spike protein S1
E: COVA309-22 heavy chain
F: COVA309-22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8144
Polymers70,5933
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-30 kcal/mol
Surface area28350 Å2
MethodPISA
3
G: Spike protein S1
H: COVA309-22 heavy chain
I: COVA309-22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8144
Polymers70,5933
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-29 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.725, 152.530, 240.786
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: Protein Spike protein S1


Mass: 23104.867 Da / Num. of mol.: 3 / Fragment: Receptor binding domain, UNP residues 333-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody COVA309-22 heavy chain


Mass: 23919.764 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody COVA309-22 light chain


Mass: 23568.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: 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.: 3 / 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
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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate, pH 6.5, 0.2 M magnesium chloride, and 20% (w/v) polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 41627 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.955 / Χ2: 0.153 / Net I/σ(I): 1.9 / Num. measured all: 277783
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.7-3.7651.64320410.452198.7
3.76-3.835.41.20920750.438199.4
3.83-3.916.41.26821240.462199.6
3.91-3.996.51.15220410.45199.9
3.99-4.076.70.93520760.461100
4.07-4.176.70.79621180.4731100
4.17-4.276.80.66820760.4831100
4.27-4.396.90.51520850.5081100
4.39-4.526.90.43820700.5161100
4.52-4.666.90.38220720.562199.6
4.66-4.836.70.38420770.557199.9
4.83-5.0260.34421070.5481100
5.02-5.257.20.33520690.5551100
5.25-5.537.30.32921010.5421100
5.53-5.877.20.36420680.5041100
5.87-6.327.20.33520810.5191100
6.32-6.966.90.25920960.529199.6
6.96-7.966.50.18320820.581199.9
7.96-10.027.30.1120690.7511100
10.02-506.80.0820991.095199.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.19.2refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 3.7→47.25 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.275 1110 4.96 %
Rwork0.2258 --
obs0.2282 22383 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14568 0 42 0 14610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214979
X-RAY DIFFRACTIONf_angle_d0.56220388
X-RAY DIFFRACTIONf_dihedral_angle_d4.0732073
X-RAY DIFFRACTIONf_chiral_restr0.0442256
X-RAY DIFFRACTIONf_plane_restr0.0042619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.860.35851460.30882518X-RAY DIFFRACTION97
3.86-4.060.31241420.28662600X-RAY DIFFRACTION100
4.06-4.320.35851380.25152623X-RAY DIFFRACTION100
4.32-4.650.25051500.20942631X-RAY DIFFRACTION100
4.65-5.120.27691130.2082677X-RAY DIFFRACTION100
5.12-5.860.24441400.21482682X-RAY DIFFRACTION100
5.86-7.380.27821340.22832700X-RAY DIFFRACTION100
7.38-47.250.22321470.1892842X-RAY DIFFRACTION99

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