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- PDB-7vzt: A human neutralizing antibody targeting SARS-CoV-2 RBD -

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Basic information

Entry
Database: PDB / ID: 7vzt
TitleA human neutralizing antibody targeting SARS-CoV-2 RBD
Components
  • GH12-Heavy
  • GH12-LIGHT
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / antigen / glycosylation / ANTIVIRAL 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 / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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: 3.41 Å
AuthorsWang, F.Z. / Wang, Y. / Tan, X.W. / Shi, R. / Yan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: GH12, glycosylation function
Authors: Wang, F.Z. / Tan, X.W. / Shi, R.
History
DepositionNov 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 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
B: GH12-Heavy
C: GH12-LIGHT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6364
Polymers68,2123
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-17 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.605, 150.605, 121.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Spike protein S1


Mass: 22434.141 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 / Production host: Eukaryota sp. (eukaryote) / References: UniProt: P0DTC2
#2: Antibody GH12-Heavy


Mass: 22773.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Eukaryota sp. (eukaryote)
#3: Antibody GH12-LIGHT


Mass: 23004.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Eukaryota sp. (eukaryote)
#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 genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
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: 5.82 Å3/Da / Density % sol: 78.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100mM HEPES (pH 7.5), 40% (v/v) Polyethylene glycol monomethyl ether 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 15881 / % possible obs: 71.9 % / Redundancy: 34.7 % / Biso Wilson estimate: 60.65 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.6
Reflection shellResolution: 3.41→49.4 Å / Num. unique obs: 15881 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
HKL-30001.18.2_3874data collection
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG,4TSA

6lzg

4tsa


Resolution: 3.41→49.3 Å / SU ML: 0.4663 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 1585 9.98 %
Rwork0.2175 14296 -
obs0.222 15881 71.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.71 Å2
Refinement stepCycle: LAST / Resolution: 3.41→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 28 0 4768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514890
X-RAY DIFFRACTIONf_angle_d1.18946679
X-RAY DIFFRACTIONf_chiral_restr0.0618749
X-RAY DIFFRACTIONf_plane_restr0.01091486
X-RAY DIFFRACTIONf_dihedral_angle_d14.1668685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.41-3.520.3674420.3119376X-RAY DIFFRACTION20.98
3.52-3.640.4117540.3172466X-RAY DIFFRACTION26.42
3.64-3.790.3747680.327639X-RAY DIFFRACTION35.51
3.79-3.960.4239930.3067803X-RAY DIFFRACTION45.64
3.96-4.170.27551320.23131199X-RAY DIFFRACTION67.36
4.17-4.430.24731830.20771672X-RAY DIFFRACTION92.8
4.43-4.770.21911950.17911785X-RAY DIFFRACTION99.9
4.77-5.250.22672030.19091816X-RAY DIFFRACTION99.9
5.25-6.010.22232030.21431812X-RAY DIFFRACTION100
6.01-7.570.27112010.23971835X-RAY DIFFRACTION99.85
7.57-49.30.25652110.19391893X-RAY DIFFRACTION99.29

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