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- PDB-8gb7: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 8gb7
TitleCrystal structure of SARS-CoV-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 / host extracellular space / viral translation / 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 / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / 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
Biological speciesMacaca mulatta (Rhesus monkey)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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
H: 20A7 Heavy chain
L: 20A7 Light chain
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5634
Polymers70,1383
Non-polymers4241
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-27 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.751, 131.421, 174.054
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: 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)
#2: 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)
#3: Protein Spike protein S1


Mass: 23104.867 Da / Num. of mol.: 1 / 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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M CaCl2, 10% ethylene glycol (v/v), and 20% polyethylene glycol 3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 62503 / % possible obs: 98.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.986 / Χ2: 0.071 / Net I/σ(I): 4.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.58-2.623.80.77628460.355188.3
2.62-2.674.30.72529350.361194.5
2.67-2.724.80.76931020.369198.3
2.72-2.785.50.70831470.384198.9
2.78-2.845.70.65731200.397199.3
2.84-2.915.80.59931570.407199.8
2.91-2.985.80.50931690.425199.8
2.98-3.065.40.41931210.469199.5
3.06-3.156.20.37131560.518199.9
3.15-3.256.90.33531730.5481100
3.25-3.377.10.29931290.591100
3.37-3.57.20.24731770.681100
3.5-3.667.10.22131600.7321100
3.66-3.8570.20431430.7951100
3.85-4.096.80.14832050.955199.8
4.09-4.416.40.1231231.194199.9
4.41-4.856.70.10131591.264199.8
4.85-5.567.50.09431651.149199.9
5.56-77.30.09131490.9631100
7-506.90.06231671.586199.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.19.2refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→42.48 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 1567 4.69 %
Rwork0.2039 --
obs0.2058 33417 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 28 182 4918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034852
X-RAY DIFFRACTIONf_angle_d0.6436606
X-RAY DIFFRACTIONf_dihedral_angle_d5.195675
X-RAY DIFFRACTIONf_chiral_restr0.045737
X-RAY DIFFRACTIONf_plane_restr0.005851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.650.43331280.33052588X-RAY DIFFRACTION89
2.65-2.740.29591360.27042817X-RAY DIFFRACTION99
2.74-2.850.32931490.24872860X-RAY DIFFRACTION99
2.85-2.980.30711520.24332904X-RAY DIFFRACTION100
2.98-3.140.28891280.26432865X-RAY DIFFRACTION100
3.14-3.340.29861320.23582895X-RAY DIFFRACTION100
3.34-3.60.26851580.20942908X-RAY DIFFRACTION100
3.6-3.960.26081380.20422935X-RAY DIFFRACTION100
3.96-4.530.18991450.15962961X-RAY DIFFRACTION100
4.53-5.70.17611390.15422991X-RAY DIFFRACTION100
5.7-42.480.21751620.1963126X-RAY DIFFRACTION100

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