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- PDB-8gpy: Crystal structure of Omicron BA.4/5 RBD in complex with a neutral... -

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Basic information

Entry
Database: PDB / ID: 8gpy
TitleCrystal structure of Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv
Components
  • Spike protein S1
  • scFv
KeywordsVIRAL PROTEIN / Omicron / crystal strcture / neutralizing antibody / scFV
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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: 2.51 Å
AuthorsGao, Y.X. / Song, Z.D. / Wang, W.M. / Guo, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870733, 81890990, 81730006, 82022002 China
Other government2018YFE0200400, 2021YFA1100900, 2021YFA1102800 China
CitationJournal: Nat Commun / Year: 2023
Title: Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection.
Authors: Yu Guo / Guangshun Zhang / Qi Yang / Xiaowei Xie / Yang Lu / Xuelian Cheng / Hui Wang / Jingxi Liang / Jielin Tang / Yuxin Gao / Hang Shang / Jun Dai / Yongxia Shi / Jiaxi Zhou / Jun Zhou / ...Authors: Yu Guo / Guangshun Zhang / Qi Yang / Xiaowei Xie / Yang Lu / Xuelian Cheng / Hui Wang / Jingxi Liang / Jielin Tang / Yuxin Gao / Hang Shang / Jun Dai / Yongxia Shi / Jiaxi Zhou / Jun Zhou / Hangtian Guo / Haitao Yang / Jianwei Qi / Lijun Liu / Shihui Ma / Biao Zhang / Qianyu Huo / Yi Xie / Junping Wu / Fang Dong / Song Zhang / Zhiyong Lou / Yan Gao / Zidan Song / Wenming Wang / Zixian Sun / Xiaoming Yang / Dongsheng Xiong / Fengjiang Liu / Xinwen Chen / Ping Zhu / Ximo Wang / Tao Cheng / Zihe Rao /
Abstract: The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, ...The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection.
History
DepositionAug 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 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
Revision 2.0Mar 13, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _entity_poly_seq.entity_id / _entity_poly_seq.num / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
C: scFv
E: scFv


Theoretical massNumber of molelcules
Total (without water)94,4814
Polymers94,4814
Non-polymers00
Water2,684149
1
A: Spike protein S1
E: scFv


Theoretical massNumber of molelcules
Total (without water)47,2412
Polymers47,2412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
C: scFv


Theoretical massNumber of molelcules
Total (without water)47,2412
Polymers47,2412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.863, 92.092, 89.270
Angle α, β, γ (deg.)90.000, 92.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Spike protein S1


Mass: 22565.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia (butterflies/moths) / References: UniProt: P0DTC2
#2: Antibody scFv


Mass: 24675.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia (butterflies/moths)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Potassium formate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 48308 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.53 Å2 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.053 / Rrim(I) all: 0.136 / Χ2: 0.954 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.62.0617310.3330.862.2360.852100
2.54-2.596.81.54216680.4410.6341.6690.649100
2.59-2.646.81.26917260.5030.5221.3730.643100
2.64-2.696.61.03516940.5350.4381.1261.065100
2.69-2.756.80.88217050.6610.3630.9550.629100
2.75-2.826.80.72916850.740.3020.790.695100
2.82-2.896.80.60917000.8140.2510.660.675100
2.89-2.966.80.4817220.8580.1980.520.672100
2.96-3.056.90.37217060.910.1530.4030.69100
3.05-3.156.80.27516980.9480.1140.2980.768100
3.15-3.266.70.24816980.7690.1050.271.093100
3.26-3.396.50.15817260.9630.0670.1720.811100
3.39-3.556.80.1516970.9660.0630.1631.343100
3.55-3.736.80.12317200.9740.0510.1341.127100
3.73-3.976.80.1116950.9780.0450.1191.24699.9
3.97-4.276.80.06917400.9850.0290.0740.934100
4.27-4.76.60.05516980.9940.0230.0591.022100
4.7-5.386.60.05817240.9880.0250.0631.149100
5.38-6.786.70.05517360.9930.0230.061.063100
6.78-506.40.07117670.9840.0310.0772.02399.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nik

4nik


Resolution: 2.51→49.6 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 3230 6.69 %
Rwork0.2149 45078 -
obs0.2173 48308 71.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.8 Å2 / Biso mean: 45.0135 Å2 / Biso min: 14.91 Å2
Refinement stepCycle: final / Resolution: 2.51→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6409 0 0 149 6558
Biso mean---34.56 -
Num. residues----828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.540.6206170.46972562739
2.54-2.580.4941260.414641944515
2.58-2.620.3493440.353161666022
2.62-2.670.2767670.32276583229
2.67-2.720.3083840.30231091117540
2.72-2.770.3407810.31357143849
2.77-2.830.26751130.30241466157954
2.83-2.890.33981270.30111603173060
2.89-2.960.30991260.29651818194465
2.96-3.030.33241400.27911952209274
3.03-3.110.27541620.27892131229378
3.11-3.20.34941580.24392391254985
3.2-3.310.24771720.26352446261890
3.31-3.420.29061860.24272549273594
3.43-3.560.2891850.22582665285098
3.56-3.720.27391830.21952679286298
3.72-3.920.26321900.20052663285398
3.92-4.170.20591970.19022712290999
4.17-4.490.19991870.16712710289799
4.49-4.940.18071920.1622692288499
4.94-5.650.24191990.17392703290299
5.65-7.120.21612000.193627152915100
7.12-49.60.21911940.18662679287398

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