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- PDB-7e88: Crystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab -

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Basic information

Entry
Database: PDB / ID: 7.0E+88
TitleCrystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab
Components
  • BD-515 Fab Heavy Chain
  • BD-515 Fab Light Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / IMMUNE SYSTEM / SARS-CoV-2 / 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 / 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 / Resolution: 3.14 Å
AuthorsGao, C. / Wei, 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
DepositionMar 1, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BD-515 Fab Heavy Chain
B: BD-515 Fab Light Chain
C: Spike protein S1
D: BD-515 Fab Heavy Chain
E: BD-515 Fab Light Chain
F: Spike protein S1
G: BD-515 Fab Heavy Chain
H: BD-515 Fab Light Chain
I: Spike protein S1
J: BD-515 Fab Heavy Chain
K: BD-515 Fab Light Chain
L: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)275,60012
Polymers275,60012
Non-polymers00
Water0
1
A: BD-515 Fab Heavy Chain
B: BD-515 Fab Light Chain
C: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)68,9003
Polymers68,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: BD-515 Fab Heavy Chain
E: BD-515 Fab Light Chain
F: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)68,9003
Polymers68,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: BD-515 Fab Heavy Chain
H: BD-515 Fab Light Chain
I: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)68,9003
Polymers68,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: BD-515 Fab Light Chain
J: BD-515 Fab Heavy Chain
K: BD-515 Fab Light Chain
L: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)92,5394
Polymers92,5394
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.708, 107.600, 108.761
Angle α, β, γ (deg.)63.340, 80.950, 66.850
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 131 or resid 137 through 216))
21(chain D and resid 3 through 216)
31(chain G and resid 3 through 216)
41(chain J and (resid 3 through 131 or resid 137 through 216))
12chain B
22chain E
32chain H
42chain K
13chain C
23chain F
33chain I
43chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNSERSER(chain A and (resid 3 through 131 or resid 137 through 216))AA3 - 1313 - 131
121GLYGLYPROPRO(chain A and (resid 3 through 131 or resid 137 through 216))AA137 - 216137 - 216
211GLNGLNPROPRO(chain D and resid 3 through 216)DD3 - 2163 - 216
311GLNGLNPROPRO(chain G and resid 3 through 216)GG3 - 2163 - 216
411GLNGLNSERSER(chain J and (resid 3 through 131 or resid 137 through 216))JJ3 - 1313 - 131
421GLYGLYPROPRO(chain J and (resid 3 through 131 or resid 137 through 216))JJ137 - 216137 - 216
112ASPASPGLYGLYchain BBB1 - 2121 - 212
212ASPASPGLYGLYchain EEE1 - 2121 - 212
312ASPASPGLYGLYchain HHH1 - 2121 - 212
412ASPASPGLYGLYchain KKK1 - 2121 - 212
113THRTHRGLYGLYchain CCC333 - 5261 - 194
213ASNASNGLYGLYchain FFF334 - 5262 - 194
313THRTHRGLYGLYchain III333 - 5261 - 194
413THRTHRGLYGLYchain LLL333 - 5261 - 194

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
BD-515 Fab Heavy Chain


Mass: 23484.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
BD-515 Fab Light Chain


Mass: 23639.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein
Spike protein S1


Mass: 21776.381 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2

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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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.3 M Ammonium sulfate, 0.1 M Potassium sodium tartrate tetrahydrate, and 25% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. obs: 65090 / % possible obs: 97.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Χ2: 0.589 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.17-3.223.50.40832730.8940.2470.4770.44498.6
3.22-3.283.50.37332690.9060.2270.4370.46498.5
3.28-3.353.50.332690.9290.1830.3520.47497.5
3.35-3.413.40.2531710.9480.1550.2960.47995.8
3.41-3.493.30.27930610.8920.1770.3320.90691.5
3.49-3.573.60.18332840.9740.1120.2150.49498.9
3.57-3.663.70.17632690.9750.1060.2060.50698.9
3.66-3.763.60.233090.9210.1230.2350.84298.6
3.76-3.873.60.12433120.9870.0740.1450.51398.5
3.87-3.993.60.14532620.9540.090.1710.86698.7
3.99-4.143.60.08732930.9930.0520.1020.54499.1
4.14-4.33.60.07232710.9940.0430.0840.58598
4.3-4.53.40.06332270.9950.0390.0740.61196.4
4.5-4.733.50.05631920.9950.0350.0670.60895.8
4.73-5.033.70.05332720.9960.0320.0620.60499.1
5.03-5.423.70.0533250.9960.030.0580.57499.2
5.42-5.963.60.04932740.9960.0290.0570.54798.9
5.96-6.823.30.04532220.9960.0280.0530.55996
6.82-8.593.60.03933050.9970.0240.0460.56299.3
8.59-503.50.03332300.9980.020.0390.62597

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CH4

7ch4


Resolution: 3.14→49.43 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 30.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 2012 3.1 %
Rwork0.2173 62992 -
obs0.2185 65004 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.05 Å2 / Biso mean: 89.327 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.14→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18863 0 0 0 18863
Num. residues----2446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3762X-RAY DIFFRACTION13.227TORSIONAL
12D3762X-RAY DIFFRACTION13.227TORSIONAL
13G3762X-RAY DIFFRACTION13.227TORSIONAL
14J3762X-RAY DIFFRACTION13.227TORSIONAL
21B4006X-RAY DIFFRACTION13.227TORSIONAL
22E4006X-RAY DIFFRACTION13.227TORSIONAL
23H4006X-RAY DIFFRACTION13.227TORSIONAL
24K4006X-RAY DIFFRACTION13.227TORSIONAL
31C3551X-RAY DIFFRACTION13.227TORSIONAL
32F3551X-RAY DIFFRACTION13.227TORSIONAL
33I3551X-RAY DIFFRACTION13.227TORSIONAL
34L3551X-RAY DIFFRACTION13.227TORSIONAL
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 (%)
3.14-3.220.41771290.34553875400484
3.22-3.310.39211560.31674529468598
3.31-3.40.33471290.29874506463596
3.4-3.510.33231440.29444356450094
3.51-3.640.30451430.27034610475399
3.64-3.780.31751460.27834574472098
3.78-3.960.30271550.26164565472098
3.96-4.170.24071350.20964669480499
4.17-4.430.24161510.18084508465997
4.43-4.770.21281360.16684505464196
4.77-5.250.21171480.16594600474899
5.25-60.23571500.18644633478399
6.01-7.560.26111420.21694516465897
7.56-49.430.1971480.194546469497
Refinement TLS params.Method: refined / Origin x: -0.7993 Å / Origin y: 23.3449 Å / Origin z: 21.2996 Å
111213212223313233
T0.6375 Å2-0.0562 Å20.0074 Å2-0.6028 Å2-0.0629 Å2--0.6764 Å2
L0.2898 °2-0.0865 °2-0.2025 °2-0.2367 °2-0.0007 °2--0.3038 °2
S-0.0003 Å °-0.0259 Å °0.0243 Å °-0.0162 Å °0.0311 Å °-0.0116 Å °-0.0703 Å °0.0221 Å °-0.029 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 216
2X-RAY DIFFRACTION1allB1 - 212
3X-RAY DIFFRACTION1allC333 - 526
4X-RAY DIFFRACTION1allD2 - 216
5X-RAY DIFFRACTION1allE1 - 212
6X-RAY DIFFRACTION1allF334 - 526
7X-RAY DIFFRACTION1allG2 - 216
8X-RAY DIFFRACTION1allH1 - 212
9X-RAY DIFFRACTION1allI333 - 526
10X-RAY DIFFRACTION1allJ3 - 216
11X-RAY DIFFRACTION1allK1 - 212
12X-RAY DIFFRACTION1allL333 - 526

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