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- PDB-7jx3: Mapping neutralizing and immunodominant sites on the SARS-CoV-2 s... -

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Basic information

Entry
Database: PDB / ID: 7jx3
TitleMapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Components
  • (Heavy chain of Fab domain of monoclonal antibody ...) x 3
  • (Light chain of Fab domain of monoclonal antibody ...) x 3
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / neutralizing monoclonal 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSnell, G. / Czudnochowski, N. / Rosen, L.E. / Nix, J.C. / Corti, D. / Veesler, D. / Park, Y.J. / Walls, A.C. / Tortorici, M.A. / Cameroni, E. ...Snell, G. / Czudnochowski, N. / Rosen, L.E. / Nix, J.C. / Corti, D. / Veesler, D. / Park, Y.J. / Walls, A.C. / Tortorici, M.A. / Cameroni, E. / Pinto, D. / Beltramello, M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120553 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Seattle Structural Genomics Center for Infectious Diseases (SSGCID) United States
CitationJournal: Cell / Year: 2020
Title: Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
Authors: Luca Piccoli / Young-Jun Park / M Alejandra Tortorici / Nadine Czudnochowski / Alexandra C Walls / Martina Beltramello / Chiara Silacci-Fregni / Dora Pinto / Laura E Rosen / John E Bowen / ...Authors: Luca Piccoli / Young-Jun Park / M Alejandra Tortorici / Nadine Czudnochowski / Alexandra C Walls / Martina Beltramello / Chiara Silacci-Fregni / Dora Pinto / Laura E Rosen / John E Bowen / Oliver J Acton / Stefano Jaconi / Barbara Guarino / Andrea Minola / Fabrizia Zatta / Nicole Sprugasci / Jessica Bassi / Alessia Peter / Anna De Marco / Jay C Nix / Federico Mele / Sandra Jovic / Blanca Fernandez Rodriguez / Sneha V Gupta / Feng Jin / Giovanni Piumatti / Giorgia Lo Presti / Alessandra Franzetti Pellanda / Maira Biggiogero / Maciej Tarkowski / Matteo S Pizzuto / Elisabetta Cameroni / Colin Havenar-Daughton / Megan Smithey / David Hong / Valentino Lepori / Emiliano Albanese / Alessandro Ceschi / Enos Bernasconi / Luigia Elzi / Paolo Ferrari / Christian Garzoni / Agostino Riva / Gyorgy Snell / Federica Sallusto / Katja Fink / Herbert W Virgin / Antonio Lanzavecchia / Davide Corti / David Veesler /
Abstract: Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. ...Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.
History
DepositionAug 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.3Oct 18, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.grant_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Light chain of Fab domain of monoclonal antibody S309
A: Heavy chain of Fab domain of monoclonal antibody S309
D: Light chain of Fab domain of monoclonal antibody S2H14
C: Heavy chain of Fab domain of monoclonal antibody S2H14
L: Light chain of Fab domain of monoclonal antibody S304
H: Heavy chain of Fab domain of monoclonal antibody S304
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,4348
Polymers165,2137
Non-polymers2211
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16350 Å2
ΔGint-86 kcal/mol
Surface area63540 Å2
Unit cell
Length a, b, c (Å)79.540, 127.780, 192.280
Angle α, β, γ (deg.)90.000, 96.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 6 types, 6 molecules BADCLH

#1: Antibody Light chain of Fab domain of monoclonal antibody S309


Mass: 23204.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of Fab domain of monoclonal antibody S309


Mass: 24573.471 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 Light chain of Fab domain of monoclonal antibody S2H14


Mass: 23139.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Heavy chain of Fab domain of monoclonal antibody S2H14


Mass: 24246.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody Light chain of Fab domain of monoclonal antibody S304


Mass: 23370.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody Heavy chain of Fab domain of monoclonal antibody S304


Mass: 23729.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars / Non-polymers , 3 types, 27 molecules R

#7: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


Mass: 22948.783 Da / Num. of mol.: 1 / Fragment: Receptor binding domain (UNP residues 328-531)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#8: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 16.2% w/v PEG4000, 0.09 M sodium citrate, pH 6.0, 0.18 M ammonium acetate, 0.02 M potassium acetate, 0.01 MES, pH 6, 1.5% v/v pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 7, 2020
RadiationMonochromator: double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.65→47.75 Å / Num. obs: 55237 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.079 / Rrim(I) all: 0.215 / Net I/σ(I): 8.7 / Num. measured all: 406155
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
2.65-2.736.82.4183068245030.390.9992.6190.799.9
11.24-47.756.90.04449537140.9970.0180.04737.693.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6M0J

6m0j


Resolution: 2.65→47.5 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.899 / SU B: 53.058 / SU ML: 0.439 / SU R Cruickshank DPI: 0.9723 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.972 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 2586 4.7 %RANDOM
Rwork0.2578 ---
obs0.2591 52027 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.18 Å2 / Biso mean: 66.749 Å2 / Biso min: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å21.38 Å2
2---1.91 Å20 Å2
3---0.88 Å2
Refinement stepCycle: final / Resolution: 2.65→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11484 0 14 25 11523
Biso mean--90.07 46.58 -
Num. residues----1512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01311793
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710432
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.6516069
X-RAY DIFFRACTIONr_angle_other_deg1.2231.57224365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.10151504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60322.877511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.949151833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2731547
X-RAY DIFFRACTIONr_chiral_restr0.060.21561
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022433
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 159 -
Rwork0.412 3341 -
all-3500 -
obs--86.19 %
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)
11.1155-0.17751.98590.5402-0.05265.5218-0.06450.148-0.19810.07690.12560.08-0.2486-0.1253-0.06110.02780.0403-0.00810.71440.00390.091-5.226-19.0811.171
21.0687-0.08071.4290.95381.13054.4383-0.24640.08450.08460.0054-0.10860.2116-0.5134-0.530.35490.09690.13550.00470.71730.09030.1697-13.499-7.1222.616
33.7858-0.2109-1.81571.96270.25992.98340.14290.05630.15010.2348-0.0821-0.0084-0.2141-0.0027-0.06080.29250.0623-0.11810.38430.03120.079821.812-15.17656.042
41.2165-2.0801-0.3313.65920.57110.0930.0204-0.06540.0769-0.18390.0072-0.1696-0.0055-0.0281-0.02760.27230.0817-0.01370.77550.03560.117955.365-47.69529.526
53.0404-2.8748-1.22353.69391.18080.4963-0.2248-0.31920.21710.22060.2991-0.47690.09940.1524-0.07430.29240.134-0.09270.90090.02420.255566.147-43.51643.692
60.08130.1631-0.09475.5716-3.16441.80840.00370.0559-0.0833-0.16880.19690.33750.126-0.1869-0.20060.5593-0.0646-0.1990.5439-0.03590.18944.817-49.33782.657
70.16360.3949-0.23745.6138-1.85190.69680.0809-0.053-0.13650.1395-0.2461-0.2168-0.07290.10680.16530.5222-0.0966-0.17230.42750.03890.141117.574-48.24295.129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 213
2X-RAY DIFFRACTION2A1 - 228
3X-RAY DIFFRACTION3R332 - 527
4X-RAY DIFFRACTION4C1 - 227
5X-RAY DIFFRACTION5D1 - 213
6X-RAY DIFFRACTION6H2 - 221
7X-RAY DIFFRACTION7L1 - 214

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