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

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Basic information

Entry
Database: PDB / ID: 7jxd
TitleMapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Components(S2A4 antigen-binding (Fab) fragment) x 2
KeywordsIMMUNE SYSTEM / fusion protein / neutralizing antibody / sarbecovirus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsPark, Y.J. / Tortorici, M.A. / Walls, A.C. / Czudnochowski, N. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Snell, G. / Veesler, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 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 27, 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 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S2A4 antigen-binding (Fab) fragment
B: S2A4 antigen-binding (Fab) fragment
C: S2A4 antigen-binding (Fab) fragment
D: S2A4 antigen-binding (Fab) fragment


Theoretical massNumber of molelcules
Total (without water)95,3824
Polymers95,3824
Non-polymers00
Water1,874104
1
A: S2A4 antigen-binding (Fab) fragment
B: S2A4 antigen-binding (Fab) fragment


Theoretical massNumber of molelcules
Total (without water)47,6912
Polymers47,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-19 kcal/mol
Surface area19250 Å2
MethodPISA
2
C: S2A4 antigen-binding (Fab) fragment
D: S2A4 antigen-binding (Fab) fragment


Theoretical massNumber of molelcules
Total (without water)47,6912
Polymers47,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-23 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.091, 63.285, 113.895
Angle α, β, γ (deg.)90.000, 103.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody S2A4 antigen-binding (Fab) fragment


Mass: 24558.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody S2A4 antigen-binding (Fab) fragment


Mass: 23132.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2 M ammonium sulfate, 0.1 M sodium cacodylate/HCl, pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 24724 / % possible obs: 88 % / Redundancy: 8.7 % / Biso Wilson estimate: 41.06 Å2 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.043 / Rrim(I) all: 0.133 / Χ2: 1 / Net I/σ(I): 7.2 / Num. measured all: 215006
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5460.3728260.9360.1470.4020.73659.6
2.54-2.596.40.358880.9430.1360.3780.69963.5
2.59-2.646.80.3379270.9720.1270.3610.75166.8
2.64-2.696.90.3149690.9660.1180.3370.9568.1
2.69-2.757.40.2789760.9670.1020.2970.82371.8
2.75-2.827.40.26510480.9760.0980.2830.89374.4
2.82-2.897.70.24811040.9780.090.2650.90279.4
2.89-2.967.80.21711930.9850.0790.2321.03384
2.96-3.058.20.22212660.9880.0780.2360.98793
3.05-3.158.40.19713770.990.070.211.02997.7
3.15-3.268.90.17614080.9910.0620.1871.02899.5
3.26-3.399.20.16313920.9930.0570.1731.06699.9
3.39-3.559.10.15413840.9920.0540.1641.13199.9
3.55-3.739.70.1514160.9890.0520.1591.14999.9
3.73-3.9710.20.13714020.9910.0460.1451.05499.9
3.97-4.2710.20.11914080.9910.040.1261.26999.9
4.27-4.79.60.1114060.9910.0380.1170.812100
4.7-5.3810.10.10414410.9930.0350.110.756100
5.38-6.789.90.09714180.9940.0330.1021.064100
6.78-509.60.08414750.9960.030.091.1899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.51 Å
Translation2.5 Å46.51 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
DENZOdata reduction
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NB8

6nb8


Resolution: 2.5→46.51 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1208 4.89 %
Rwork0.2033 23471 -
obs0.2061 24679 86.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.07 Å2 / Biso mean: 60.5327 Å2 / Biso min: 39.92 Å2
Refinement stepCycle: final / Resolution: 2.5→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6423 0 0 104 6527
Biso mean---51.77 -
Num. residues----858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.60.3789740.29981703177757
2.6-2.720.35921190.28981985210467
2.72-2.860.32241200.27082209232974
2.86-3.040.38611300.27472520265084
3.04-3.280.34981320.24812964309698
3.28-3.610.24831550.210529763131100
3.61-4.130.23271490.189830043153100
4.13-5.20.21841540.154430303184100
5.2-46.510.21761750.174730803255100
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)
12.12550.26390.84241.53740.66941.2001-0.10810.1745-0.0802-0.01980.0785-0.0336-0.0749-0.05320.00930.2027-0.0224-0.00270.9982-0.02660.3111-13.0393-9.116335.2067
23.70020.20660.31672.3108-0.67861.29380.06730.02640.01110.18710.04340.0792-0.3074-0.0771-0.07970.22740.0173-0.05311.0051-0.01890.3124-26.5392-11.293652.5213
30.1214-0.28490.52891.3164-1.24912.7657-0.09790.5686-0.19810.0309-0.0812-0.04820.22680.19880.15180.3061-0.04460.07420.845-0.04170.544412.2521-15.753360.6792
41.32570.1005-0.79633.5516-0.95592.2594-0.0086-0.0635-0.14090.01510.1899-0.09040.0246-0.0837-0.16810.2706-0.0077-0.05090.916-0.03830.32714.4552-6.266271.4126
51.8761-0.14190.16130.66170.08790.1291-0.024-0.2226-0.04730.1305-0.06880.2126-0.0222-0.0142-0.00940.1561-0.0071-0.08751.14210.00280.362216.6787-13.740225.1248
64.24280.34830.60511.13810.07711.07730.26070.46640.5123-0.1608-0.12180.3098-0.1598-0.16770.17680.19320.0698-0.15651.2654-0.06680.5142.2844-9.24959.0859
70.4507-0.75030.44082.0593-2.26693.7181-0.1756-0.09170.0863-0.1465-0.1493-0.0835-0.0317-0.01480.32760.3871-0.0231-0.09611.27120.01860.559437.5641-8.2638-6.0882
81.0078-0.8597-1.1644.41890.61242.78160.08110.4301-0.293-0.2546-0.04160.31920.0347-0.40210.01260.40670.0264-0.0541.1410.04620.502225.1585-17.5741-9.1273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 119 )A1 - 119
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 111 )B1 - 111
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 220 )A120 - 220
4X-RAY DIFFRACTION4chain 'B' and (resid 112 through 214 )B112 - 214
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 119 )C1 - 119
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 113 )D1 - 113
7X-RAY DIFFRACTION7chain 'C' and (resid 120 through 220 )C120 - 220
8X-RAY DIFFRACTION8chain 'D' and (resid 114 through 214 )D114 - 214

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