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- PDB-7xik: SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex -

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Basic information

Entry
Database: PDB / ID: 7xik
TitleSARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex
Components
  • B38 Fab heavy chain
  • B38 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / antibody / VIRAL PROTEIN / 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: 2.89 Å
AuthorsShi, R. / Wang, Y. / Wu, Z. / Han, X. / Yan, J.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
Chinese Academy of Sciences China
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex
Authors: Shi, R. / Wang, Y. / Wu, Z. / Han, X. / Yan, J.
History
DepositionApr 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
H: B38 Fab heavy chain
L: B38 Fab light chain


Theoretical massNumber of molelcules
Total (without water)73,1453
Polymers73,1453
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.959, 145.859, 144.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Spike protein S1


Mass: 25781.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Variant: omicron / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody B38 Fab heavy chain


Mass: 23521.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody B38 Fab light chain


Mass: 23842.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 15% v/v 2-Propanol, 0.1M Sodium citrate tribasic dihydrate pH 5.0, 10% Polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2022
RadiationMonochromator: LN2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.89→73.413 Å / Num. obs: 20329 / % possible obs: 99.8 % / Redundancy: 13 % / CC1/2: 0.994 / Rmerge(I) obs: 0.262 / Rpim(I) all: 0.075 / Rrim(I) all: 0.272 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.893-2.90313.61.53926131920.7230.4251.5972.1100
13.403-73.4139.90.05822502270.9990.0180.06121.592.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
Aimlessdata scaling
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7bz5

7bz5


Resolution: 2.89→73.41 Å / SU ML: 0.4179 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.263 2009 9.89 %
Rwork0.2106 18301 -
obs0.2158 20310 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.06 Å2
Refinement stepCycle: LAST / Resolution: 2.89→73.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 0 14 0 4859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534992
X-RAY DIFFRACTIONf_angle_d0.74266799
X-RAY DIFFRACTIONf_chiral_restr0.0504751
X-RAY DIFFRACTIONf_plane_restr0.0049875
X-RAY DIFFRACTIONf_dihedral_angle_d18.53471785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.970.36241430.32681264X-RAY DIFFRACTION99.93
2.97-3.050.4061390.29541310X-RAY DIFFRACTION99.79
3.05-3.140.37791410.25651299X-RAY DIFFRACTION100
3.14-3.240.29661410.25661279X-RAY DIFFRACTION99.86
3.24-3.350.32151420.25651297X-RAY DIFFRACTION99.93
3.35-3.490.32851420.23971305X-RAY DIFFRACTION100
3.49-3.650.28161330.23741305X-RAY DIFFRACTION100
3.65-3.840.28131450.22081304X-RAY DIFFRACTION100
3.84-4.080.25431420.19121295X-RAY DIFFRACTION99.72
4.08-4.390.21051450.16751301X-RAY DIFFRACTION100
4.39-4.830.20921450.15771311X-RAY DIFFRACTION99.86
4.83-5.530.20131460.16951330X-RAY DIFFRACTION100
5.53-6.970.25291540.20521336X-RAY DIFFRACTION100
6.97-73.410.23651510.21011365X-RAY DIFFRACTION97.24

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