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- PDB-7e7y: Crystal structure of the SARS-CoV-2 S RBD in complex with BD-623 Fab -

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Entry
Database: PDB / ID: 7e7y
TitleCrystal structure of the SARS-CoV-2 S RBD in complex with BD-623 Fab
Components
  • BD-623 Fab H
  • BD-623 Fab L
  • Spike protein S1
KeywordsVIRAL PROTEIN / Spike RBD Antibody
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsWei, Y. / Xiao, J.
CitationJournal: Cell Res / Year: 2021
Title: Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.
Authors: Yunlong Cao / Ayijiang Yisimayi / Yali Bai / Weijin Huang / Xiaofeng Li / Zhiying Zhang / Tianjiao Yuan / Ran An / Jing Wang / Tianhe Xiao / Shuo Du / Wenping Ma / Liyang Song / Yongzheng Li ...Authors: Yunlong Cao / Ayijiang Yisimayi / Yali Bai / Weijin Huang / Xiaofeng Li / Zhiying Zhang / Tianjiao Yuan / Ran An / Jing Wang / Tianhe Xiao / Shuo Du / Wenping Ma / Liyang Song / Yongzheng Li / Xiang Li / Weiliang Song / Jiajing Wu / Shuo Liu / Xuemei Li / Yonghong Zhang / Bin Su / Xianghua Guo / Yangyang Wei / Chuanping Gao / Nana Zhang / Yifei Zhang / Yang Dou / Xiaoyu Xu / Rui Shi / Bai Lu / Ronghua Jin / Yingmin Ma / Chengfeng Qin / Youchun Wang / Yingmei Feng / Junyu Xiao / Xiaoliang Sunney Xie /
Abstract: SARS-CoV-2 variants could induce immune escape by mutations on the receptor-binding domain (RBD) and N-terminal domain (NTD). Here we report the humoral immune response to circulating SARS-CoV-2 ...SARS-CoV-2 variants could induce immune escape by mutations on the receptor-binding domain (RBD) and N-terminal domain (NTD). Here we report the humoral immune response to circulating SARS-CoV-2 variants, such as 501Y.V2 (B.1.351), of the plasma and neutralizing antibodies (NAbs) elicited by CoronaVac (inactivated vaccine), ZF2001 (RBD-subunit vaccine) and natural infection. Among 86 potent NAbs identified by high-throughput single-cell VDJ sequencing of peripheral blood mononuclear cells from vaccinees and convalescents, near half anti-RBD NAbs showed major neutralization reductions against the K417N/E484K/N501Y mutation combination, with E484K being the dominant cause. VH3-53/VH3-66 recurrent antibodies respond differently to RBD variants, and K417N compromises the majority of neutralizing activity through reduced polar contacts with complementarity determining regions. In contrast, the 242-244 deletion (242-244Δ) would abolish most neutralization activity of anti-NTD NAbs by interrupting the conformation of NTD antigenic supersite, indicating a much less diversity of anti-NTD NAbs than anti-RBD NAbs. Plasma of convalescents and CoronaVac vaccinees displayed comparable neutralization reductions against pseudo- and authentic 501Y.V2 variants, mainly caused by E484K/N501Y and 242-244Δ, with the effects being additive. Importantly, RBD-subunit vaccinees exhibit markedly higher tolerance to 501Y.V2 than convalescents, since the elicited anti-RBD NAbs display a high diversity and are unaffected by NTD mutations. Moreover, an extended gap between the third and second doses of ZF2001 leads to better neutralizing activity and tolerance to 501Y.V2 than the standard three-dose administration. Together, these results suggest that the deployment of RBD-vaccines, through a third-dose boost, may be ideal for combating SARS-CoV-2 variants when necessary, especially for those carrying mutations that disrupt the NTD supersite.
History
DepositionFeb 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BD-623 Fab H
B: BD-623 Fab L
R: Spike protein S1
C: BD-623 Fab H
D: BD-623 Fab L
E: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)142,3556
Polymers142,3556
Non-polymers00
Water10,395577
1
A: BD-623 Fab H
B: BD-623 Fab L
R: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)71,1783
Polymers71,1783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: BD-623 Fab H
D: BD-623 Fab L
E: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)71,1783
Polymers71,1783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.817, 126.631, 138.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody BD-623 Fab H


Mass: 24041.908 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 BD-623 Fab L


Mass: 22013.398 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: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 25122.336 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 ni (cabbage looper) / References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, and 18% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.41→49.09 Å / Num. obs: 63988 / % possible obs: 98.05 % / Redundancy: 13.5 % / CC1/2: 0.998 / Net I/σ(I): 11.03
Reflection shellResolution: 2.412→2.498 Å / Num. unique obs: 5923 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CH5

7ch5


Resolution: 2.41→49.09 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1977 3.13 %
Rwork0.1973 61172 -
obs0.1987 63149 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.93 Å2 / Biso mean: 39.0369 Å2 / Biso min: 17.41 Å2
Refinement stepCycle: final / Resolution: 2.41→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9339 0 0 577 9916
Biso mean---40.52 -
Num. residues----1235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.41-2.470.32341300.25734016414691
2.47-2.540.26921420.239644014543100
2.54-2.610.32051420.232643864528100
2.61-2.70.25281420.22243904532100
2.7-2.790.24931420.217244054547100
2.79-2.910.27161430.217444084551100
2.91-3.040.26931430.227844354578100
3.04-3.20.27141430.219644264569100
3.2-3.40.25591440.206744374581100
3.4-3.660.261440.203544544598100
3.66-4.030.24451450.193644684613100
4.03-4.610.20641440.154344684612100
4.61-5.810.19171420.164352449496
5.81-49.090.20681310.19494126425787

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