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- PDB-8gb8: Crystal structure of SARS-CoV-2 BA.2 receptor binding domain in c... -

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Basic information

Entry
Database: PDB / ID: 8gb8
TitleCrystal structure of SARS-CoV-2 BA.2 receptor binding domain in complex with neutralizing antibody 20A7
Components
  • 20A7 Heavy chain
  • 20A7 Light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / antibody / spike / receptor binding domain
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLYCINE / DI(HYDROXYETHYL)ETHER / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support United States, 4items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-018675 United States
Bill & Melinda Gates FoundationINV-004923 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI167966 United States
Bill & Melinda Gates FoundationINV-010680 United States
CitationJournal: Sci Transl Med / Year: 2023
Title: Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Authors: Feng, Y. / Yuan, M. / Powers, J.M. / Hu, M. / Munt, J.E. / Arunachalam, P.S. / Leist, S.R. / Bellusci, L. / Kim, J. / Sprouse, K.R. / Adams, L.E. / Sundaramurthy, S. / Zhu, X. / Shirreff, L. ...Authors: Feng, Y. / Yuan, M. / Powers, J.M. / Hu, M. / Munt, J.E. / Arunachalam, P.S. / Leist, S.R. / Bellusci, L. / Kim, J. / Sprouse, K.R. / Adams, L.E. / Sundaramurthy, S. / Zhu, X. / Shirreff, L.M. / Mallory, M.L. / Scobey, T.D. / Moreno, A. / O'Hagan, D.T. / Kleanthous, H. / Villinger, F.J. / Veesler, D. / King, N.P. / Suthar, M.S. / Khurana, S. / Baric, R.S. / Wilson, I.A. / Pulendran, B.
History
DepositionFeb 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike protein S1
H: 20A7 Heavy chain
L: 20A7 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,97610
Polymers73,2953
Non-polymers6817
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.544, 132.184, 170.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody 20A7 Heavy chain


Mass: 23831.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Mus musculus (house mouse)
#3: Antibody 20A7 Light chain


Mass: 23201.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Mus musculus (house mouse)

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Protein / Sugars , 2 types, 2 molecules E

#1: Protein Spike protein S1


Mass: 26261.727 Da / Num. of mol.: 1 / Fragment: Receptor binding domain, UNP residues 319-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Strain: Omicron BA.2 / Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#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.: 1 / 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 , 5 types, 200 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 10% (v/v) glycerol, 5% (w/v) polyethylene glycol 3000, and 30% (v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 86216 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.99 / Χ2: 0.06 / Net I/σ(I): 5.8 / Num. measured all: 541836
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.3-2.344.11.21541360.422194.1
2.34-2.384.51.26441760.421196.9
2.38-2.4351.12342270.423199
2.43-2.485.61.02144080.411199.9
2.48-2.536.10.9642740.474199.9
2.53-2.596.40.84343520.431100
2.59-2.666.50.73243170.431100
2.66-2.736.50.56543120.4521100
2.73-2.816.30.4843780.4651100
2.81-2.95.80.35842940.512199.7
2.9-36.80.28843390.561100
3-3.1270.2243420.6721100
3.12-3.2670.18243160.788199.9
3.26-3.4470.13843451.0211100
3.44-3.656.80.11843241.3541100
3.65-3.936.70.09943221.6411100
3.93-4.336.10.08143322.063199.7
4.33-4.957.30.07443612.5291100
4.95-6.247.20.07343172.3831100
6.24-506.70.06143442.831199.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.19.2refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.1 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 2321 5.07 %
Rwork0.1995 --
obs0.201 45816 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 43 194 5033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024966
X-RAY DIFFRACTIONf_angle_d0.5436750
X-RAY DIFFRACTIONf_dihedral_angle_d5.238694
X-RAY DIFFRACTIONf_chiral_restr0.044745
X-RAY DIFFRACTIONf_plane_restr0.005871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.35891410.29472303X-RAY DIFFRACTION91
2.34-2.390.2921330.27232485X-RAY DIFFRACTION99
2.39-2.450.30561520.25542538X-RAY DIFFRACTION100
2.45-2.510.31771180.24282545X-RAY DIFFRACTION100
2.51-2.580.28551280.25052526X-RAY DIFFRACTION100
2.58-2.650.31411350.26082558X-RAY DIFFRACTION100
2.65-2.740.25921250.23032536X-RAY DIFFRACTION100
2.74-2.840.24641220.21542557X-RAY DIFFRACTION100
2.84-2.950.25511330.20762571X-RAY DIFFRACTION100
2.95-3.080.25781460.20762532X-RAY DIFFRACTION100
3.08-3.250.2551350.22182567X-RAY DIFFRACTION100
3.25-3.450.21281290.2152579X-RAY DIFFRACTION100
3.45-3.720.21081370.18862591X-RAY DIFFRACTION100
3.72-4.090.22381530.18612585X-RAY DIFFRACTION100
4.09-4.680.20371340.15532586X-RAY DIFFRACTION100
4.68-5.90.17341330.1692655X-RAY DIFFRACTION100
5.9-43.10.20061670.19262781X-RAY DIFFRACTION100

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