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- PDB-7s3n: SARS-CoV-2 S stem helix peptide bound to Fab22 -

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Basic information

Entry
Database: PDB / ID: 7s3n
TitleSARS-CoV-2 S stem helix peptide bound to Fab22
Components
  • Fab22 Heavy Chain
  • Fab22 Light Chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Spike / Fusion / Antibody / 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 / 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 speciesMus musculus (house mouse)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGoldsmith, J.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127521 United States
CitationJournal: Cell Rep / Year: 2021
Title: Stabilized coronavirus spike stem elicits a broadly protective antibody.
Authors: Ching-Lin Hsieh / Anne P Werner / Sarah R Leist / Laura J Stevens / Ester Falconer / Jory A Goldsmith / Chia-Wei Chou / Olubukola M Abiona / Ande West / Kathryn Westendorf / Krithika ...Authors: Ching-Lin Hsieh / Anne P Werner / Sarah R Leist / Laura J Stevens / Ester Falconer / Jory A Goldsmith / Chia-Wei Chou / Olubukola M Abiona / Ande West / Kathryn Westendorf / Krithika Muthuraman / Ethan J Fritch / Kenneth H Dinnon / Alexandra Schäfer / Mark R Denison / James D Chappell / Ralph S Baric / Barney S Graham / Kizzmekia S Corbett / Jason S McLellan /
Abstract: Current coronavirus (CoV) vaccines primarily target immunodominant epitopes in the S1 subunit, which are poorly conserved and susceptible to escape mutations, thus threatening vaccine efficacy. Here, ...Current coronavirus (CoV) vaccines primarily target immunodominant epitopes in the S1 subunit, which are poorly conserved and susceptible to escape mutations, thus threatening vaccine efficacy. Here, we use structure-guided protein engineering to remove the S1 subunit from the Middle East respiratory syndrome (MERS)-CoV spike (S) glycoprotein and develop stabilized stem (SS) antigens. Vaccination with MERS SS elicits cross-reactive β-CoV antibody responses and protects mice against lethal MERS-CoV challenge. High-throughput screening of antibody-secreting cells from MERS SS-immunized mice led to the discovery of a panel of cross-reactive monoclonal antibodies. Among them, antibody IgG22 binds with high affinity to both MERS-CoV and severe acute respiratory syndrome (SARS)-CoV-2 S proteins, and a combination of electron microscopy and crystal structures localizes the epitope to a conserved coiled-coil region in the S2 subunit. Passive transfer of IgG22 protects mice against both MERS-CoV and SARS-CoV-2 challenge. Collectively, these results provide a proof of principle for cross-reactive CoV antibodies and inform the development of pan-CoV vaccines and therapeutic antibodies.
History
DepositionSep 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 17, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Aug 10, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[1][3] / _cell.angle_beta ..._atom_sites.fract_transf_matrix[1][3] / _cell.angle_beta / _cell.volume / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_number_of_molecules / _entity.src_method / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_src_gen.entity_id / _entity_src_gen.pdbx_end_seq_num / _pdbx_entity_src_syn.entity_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_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_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_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_comp_id / _pdbx_struct_sheet_hbond.range_2_label_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_comp_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_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Sequence discrepancy / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
H: Fab22 Heavy Chain
L: Fab22 Light Chain


Theoretical massNumber of molelcules
Total (without water)50,0193
Polymers50,0193
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-33 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.246, 73.080, 89.043
Angle α, β, γ (deg.)90.000, 100.500, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein/peptide Spike glycoprotein


Mass: 2303.479 Da / Num. of mol.: 1 / Fragment: stem helix peptide (UNP residues 1146-1164) / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#2: Antibody Fab22 Heavy Chain


Mass: 23892.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Fab22 Light Chain


Mass: 23822.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate, pH 5.5, 23% PEG8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→87.55 Å / Num. obs: 38944 / % possible obs: 97.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.51 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.1
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2343 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
Cootmodel building
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7M53

7m53


Resolution: 1.9→43.78 Å / SU ML: 0.1817 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.1766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 1937 4.98 %
Rwork0.2048 36981 -
obs0.2062 38918 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 0 325 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693511
X-RAY DIFFRACTIONf_angle_d0.95174783
X-RAY DIFFRACTIONf_chiral_restr0.0592544
X-RAY DIFFRACTIONf_plane_restr0.0072611
X-RAY DIFFRACTIONf_dihedral_angle_d16.1881277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27051240.26762558X-RAY DIFFRACTION93.71
1.95-20.27441380.25232567X-RAY DIFFRACTION95.58
2-2.060.28011340.24262471X-RAY DIFFRACTION91.89
2.06-2.130.24791250.23172610X-RAY DIFFRACTION95.53
2.13-2.20.24611370.23172605X-RAY DIFFRACTION97.55
2.2-2.290.24791460.22522684X-RAY DIFFRACTION98.68
2.29-2.390.26891400.23462651X-RAY DIFFRACTION98.83
2.39-2.520.26591420.23842659X-RAY DIFFRACTION97.46
2.52-2.680.25811280.22752677X-RAY DIFFRACTION98.91
2.68-2.880.24431530.21642692X-RAY DIFFRACTION99.37
2.88-3.170.21131320.2162692X-RAY DIFFRACTION98.78
3.17-3.630.21571230.1912724X-RAY DIFFRACTION99.06
3.63-4.580.22341660.16282662X-RAY DIFFRACTION98.95
4.58-43.780.21411490.18282729X-RAY DIFFRACTION98.19
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.375563883682.37212198003-0.9187176646436.501891599741.679496232984.887548950050.366783406917-0.284960946705-0.9165867401040.8096030239220.023904519679-1.490712078170.5580694323512.104103019-0.5695590454510.901598176579-0.0183183302798-0.4501408342230.84584052912-0.1011474699290.51151966191815.332732050526.277632620440.0526249988
21.669610838240.0276937547066-0.3459305140372.20361736109-0.4060294583445.493123693810.13655955226-0.269600111589-0.003411853384270.913262393209-0.0428739710325-0.05311998469250.07351046770670.295086010428-0.09582708433930.52956594362-0.0476386251037-0.005063051047240.275406867397-0.06330920757340.1926689684932.0844010040631.976634909526.3471668963
31.73970602383-0.09312278168420.1542140152661.90857434326-0.03676736395872.777739831790.15421554906-0.4075544869180.04618209717021.11060243920.09791997674550.1903242904370.1425262990890.188586545968-0.1668665167010.673595420352-0.02501758545480.01878590191610.2552573169-0.02954946270660.1286318296-1.9192750513325.944426220326.2336062061
43.157055476220.532892320932-0.7940677053143.321837768050.1778635218071.92182906451-0.1089286813440.0283645637364-0.200714163710.258827079921-0.07319285038830.5926969988750.199956700189-0.2111248515960.170310391890.211769461899-0.0347616086020.05951563552180.154781766719-0.01032107966160.229374017962-20.680437484119.2959922845.09335456749
51.90624478384-0.02899666913710.04826361644082.07856825420.03652362917553.089112889660.0969251329253-0.297206285634-0.1745529165910.679589655445-0.0719575259565-0.1413599336450.7522526014420.195983528573-0.05165350830251.051262966390.0929923825146-0.09127404917750.356518935570.04319638567620.2326758394331.077939875448.4540684908432.7497231062
61.112369611010.6538241547261.238051853571.239437648631.016095409452.613091515150.140118112493-0.254508122951-0.5143251132340.5976421254660.35528989456-0.7697758237820.8512582036830.526813523103-0.1300839485970.8497450519810.0599907392696-0.02971460317850.2810722790320.1269275096010.189573823586-0.1209350731167.5953700459923.4262318765
72.52515571552-0.04662766663190.8267923828513.771580814040.07505473709844.313252413210.01185442365060.0755699966662-0.09321390483210.201886268624-0.0392251995003-0.00278984307628-0.1003262962370.1655412403050.05183296452770.223360313943-0.01943589922910.04543402874290.1466955650650.02002599108570.145075354811-13.12460300837.86350714733-3.04248170019
82.324231743270.2542401493820.9601422103844.22659445582-0.2824425360745.55120230980.07000713794820.0383142958156-0.1611685501760.1695085945960.01034339588380.188467763933-0.1332966363510.0585348532143-0.02041199338920.1930446921350.01061441248190.06187372325240.134837730972-0.004203041885280.194607453589-14.7457954985.93695248114-3.42913539978
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1147 through 1156 )AA1147 - 11561 - 10
22chain 'H' and (resid 3 through 93 )HB3 - 931 - 91
33chain 'H' and (resid 94 through 130 )HB94 - 13092 - 128
44chain 'H' and (resid 131 through 225 )HB131 - 225129 - 217
55chain 'L' and (resid 3 through 98 )LC3 - 981 - 93
66chain 'L' and (resid 99 through 120 )LC99 - 12094 - 115
77chain 'L' and (resid 121 through 170 )LC121 - 170116 - 165
88chain 'L' and (resid 171 through 218 )LC171 - 218166 - 213

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