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- PDB-7y3o: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7y3o
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody BIOLS56
Components
  • Heavy chain of BIOLS56
  • Light chain of BIOLS56
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRao, X. / Gao, F. / Wu, Y. / Gao, F.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Authors: Rao, X. / Zhao, R. / Tong, Z. / Guo, S. / Peng, W. / Liu, K. / Li, S. / Wu, L. / Tong, J. / Chai, Y. / Han, P. / Wang, F. / Jia, P. / Li, Z. / Zhao, X. / Li, D. / Zhang, R. / Zhang, X. / ...Authors: Rao, X. / Zhao, R. / Tong, Z. / Guo, S. / Peng, W. / Liu, K. / Li, S. / Wu, L. / Tong, J. / Chai, Y. / Han, P. / Wang, F. / Jia, P. / Li, Z. / Zhao, X. / Li, D. / Zhang, R. / Zhang, X. / Zou, W. / Li, W. / Wang, Q. / Gao, G.F. / Wu, Y. / Dai, L. / Gao, F.
History
DepositionJun 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: 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: Heavy chain of BIOLS56
L: Light chain of BIOLS56
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4924
Polymers69,2713
Non-polymers2211
Water10,881604
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-20 kcal/mol
Surface area28390 Å2
Unit cell
Length a, b, c (Å)47.230, 74.839, 214.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Heavy chain of BIOLS56


Mass: 24154.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain of BIOLS56


Mass: 23343.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 21772.391 Da / Num. of mol.: 1 / Fragment: RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / 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: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Imidazole malate, pH 7.0, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 45625 / % possible obs: 99.96 % / Redundancy: 12.6 % / Biso Wilson estimate: 36.25 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 1.189 / Num. unique obs: 5159

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13-2998refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG, 4TSA

6lzg

4tsa


Resolution: 2.1→46.13 Å / SU ML: 0.2684 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.427 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.229 2268 4.98 %
Rwork0.1829 43275 -
obs0.1852 45543 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4889 0 0 604 5493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695021
X-RAY DIFFRACTIONf_angle_d0.85446842
X-RAY DIFFRACTIONf_chiral_restr0.0523756
X-RAY DIFFRACTIONf_plane_restr0.0054879
X-RAY DIFFRACTIONf_dihedral_angle_d3.17172954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.34171390.25312552X-RAY DIFFRACTION94.72
2.14-2.190.30441480.26552641X-RAY DIFFRACTION100
2.19-2.250.40471370.33592667X-RAY DIFFRACTION99.96
2.25-2.310.40171470.3312643X-RAY DIFFRACTION99.96
2.31-2.380.28421440.22882681X-RAY DIFFRACTION100
2.38-2.450.26971490.20912677X-RAY DIFFRACTION100
2.45-2.540.26741310.20022672X-RAY DIFFRACTION99.93
2.54-2.640.27471240.20772719X-RAY DIFFRACTION100
2.64-2.760.25841290.20122722X-RAY DIFFRACTION100
2.76-2.910.26251520.20072668X-RAY DIFFRACTION100
2.91-3.090.24871570.19382687X-RAY DIFFRACTION99.96
3.09-3.330.2411600.18362699X-RAY DIFFRACTION100
3.33-3.660.21171300.17582758X-RAY DIFFRACTION100
3.66-4.190.21410.15492755X-RAY DIFFRACTION100
4.19-5.280.16351300.12652801X-RAY DIFFRACTION100
5.28-46.130.17131500.1572933X-RAY DIFFRACTION99.84

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