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

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Basic information

Entry
Database: PDB / ID: 7jxc
TitleMapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
Components(S2H14 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: 2.47 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
H: S2H14 antigen-binding (Fab) fragment
L: S2H14 antigen-binding (Fab) fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4013
Polymers47,9862
Non-polymers4141
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-20 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.439, 70.680, 115.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody S2H14 antigen-binding (Fab) fragment


Mass: 24933.824 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 S2H14 antigen-binding (Fab) fragment


Mass: 23052.219 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: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M magnesium acetate, 20% w/v PEG3350

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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: 2.47→60.302 Å / Num. obs: 17105 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 38.32 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.092 / Rsym value: 0.084 / Net I/av σ(I): 7.3 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.473-2.6160.342.224300.150.3730.3499.2
2.61-2.7660.255323090.1120.2790.25599.6
2.76-2.965.50.1714.421980.0790.1880.17199.8
2.96-3.196.10.125620370.0540.1360.12599.8
3.19-3.55.70.0957.318990.0430.1050.09599.8
3.5-3.915.80.0758.917150.0340.0830.07599.9
3.91-4.525.90.05911.215250.0260.0640.05999.8
4.52-5.535.80.0581113200.0260.0630.05899.9
5.53-7.825.40.05611.310410.0260.0620.056100
7.82-70.685.20.04912.66310.0220.0540.04999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.96 Å60.3 Å
Translation3.96 Å60.3 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NB8

6nb8


Resolution: 2.47→60.3 Å / SU ML: 0.2569 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 877 5.14 %
Rwork0.1871 16193 -
obs0.1893 17070 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.97 Å2
Refinement stepCycle: LAST / Resolution: 2.47→60.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 28 99 3299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353274
X-RAY DIFFRACTIONf_angle_d0.73164457
X-RAY DIFFRACTIONf_chiral_restr0.0485510
X-RAY DIFFRACTIONf_plane_restr0.005565
X-RAY DIFFRACTIONf_dihedral_angle_d8.8559470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.630.31211470.22972620X-RAY DIFFRACTION98.75
2.63-2.830.26451450.21852669X-RAY DIFFRACTION99.58
2.83-3.120.28931410.2022652X-RAY DIFFRACTION99.68
3.12-3.570.23621380.18822686X-RAY DIFFRACTION99.72
3.57-4.490.21321370.16242730X-RAY DIFFRACTION99.69
4.49-60.30.17951690.18312836X-RAY DIFFRACTION99.77
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)
14.216978141381.50586463148-0.6715707202362.914568302480.3589133407023.128758393810.0462110458701-0.9464452646420.3337395583060.218546683416-0.04617585095880.06164661006840.1643609000660.4951742771540.02595140515960.247367782028-0.008232763177-0.02918882268330.505480239759-0.002675518017020.30081363282430.581633501954.721666147867.6793064064
22.785363910990.3314093152840.6857263494053.42410098040.3569937998354.471908978230.04550805977880.190824373527-0.172964600355-0.1903739506580.171763754939-0.05116549726220.203314195654-0.0270828561962-0.1930369329350.284261832127-0.0169668476939-0.01478731321780.1732544219280.01243520047230.22365891572523.748051691354.602792063227.9934516512
32.33950466610.1769649152981.297058502154.60247997049-0.3299875947544.858408406020.0804183961778-0.320959135824-0.5358410445460.4973555769370.0313222384193-0.2327728890290.459296196164-0.0430162092514-0.1016769479130.3532630832510.04137526045360.03817614485920.2810628387060.09310627955270.33308604154427.112504211332.660813804262.2489441001
43.570032117290.783179991121-2.027372736662.46090819524-0.4117496482163.485003599980.0245139071970.0185788520191-0.193063248535-0.01489085358410.0592262298075-0.03708564683260.001044174578710.148912688906-0.08592259971360.207643205145-0.00387223858183-0.02272218756980.179880661445-0.04058535977910.21660889093533.285094711842.714677709933.4378043938
50.01776582065850.008514676241680.008651040329720.000769635432320.008142416575570.01907948404260.182772147426-0.08839611969620.238320589903-0.1215810025010.2311708102650.1629281417140.1350118330210.158574920165-0.0005448755170970.7031853806930.00377946814808-0.02267650588530.5536165751620.1018099300570.82605319449222.864153687843.057718102452.1305120994
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 126 )HA1 - 1261 - 114
22chain 'H' and (resid 127 through 227 )HA127 - 227115 - 215
33chain 'L' and (resid 2 through 111 )LB2 - 1111 - 110
44chain 'L' and (resid 112 through 214 )LB112 - 214111 - 213
55chain 'L' and (resid 301 through 301 )LC301

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