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- PDB-7e5y: Molecular basis for neutralizing antibody 2B11 targeting SARS-CoV... -

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Basic information

Entry
Database: PDB / ID: 7e5y
TitleMolecular basis for neutralizing antibody 2B11 targeting SARS-CoV-2 RBD
Components
  • 2B11 Fab Heavy chain
  • 2B11 Fab Light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / Complex / 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 / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsWu, H. / Yu, F. / Wang, Q.S. / Zhou, H. / Wang, W.W. / Zhao, T. / Pan, Y.B. / Yang, X.M.
CitationJournal: Cell Discov / Year: 2021
Title: Screening of potent neutralizing antibodies against SARS-CoV-2 using convalescent patients-derived phage-display libraries.
Authors: Pan, Y. / Du, J. / Liu, J. / Wu, H. / Gui, F. / Zhang, N. / Deng, X. / Song, G. / Li, Y. / Lu, J. / Wu, X. / Zhan, S. / Jing, Z. / Wang, J. / Yang, Y. / Liu, J. / Chen, Y. / Chen, Q. / ...Authors: Pan, Y. / Du, J. / Liu, J. / Wu, H. / Gui, F. / Zhang, N. / Deng, X. / Song, G. / Li, Y. / Lu, J. / Wu, X. / Zhan, S. / Jing, Z. / Wang, J. / Yang, Y. / Liu, J. / Chen, Y. / Chen, Q. / Zhang, H. / Hu, H. / Duan, K. / Wang, M. / Wang, Q. / Yang, X.
History
DepositionFeb 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Spike protein S1
L: 2B11 Fab Light chain
H: 2B11 Fab Heavy chain
A: Spike protein S1
B: 2B11 Fab Light chain
C: 2B11 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)144,0396
Polymers144,0396
Non-polymers00
Water00
1
R: Spike protein S1
L: 2B11 Fab Light chain
H: 2B11 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)72,0193
Polymers72,0193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-30 kcal/mol
Surface area26830 Å2
MethodPISA
2
A: Spike protein S1
B: 2B11 Fab Light chain
C: 2B11 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)72,0193
Polymers72,0193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-25 kcal/mol
Surface area26790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.760, 152.600, 177.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: 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: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody 2B11 Fab Light chain


Mass: 23573.961 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: Antibody 2B11 Fab Heavy chain


Mass: 23323.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 12% w/v PEG 8000, and 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.59→51.33 Å / Num. obs: 24257 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.05 / Rrim(I) all: 0.158 / Net I/σ(I): 10.9 / Num. measured all: 238965
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
3.59-3.68101.3491764817660.8040.4441.4211.899.9
16.06-51.335.80.05117032930.9990.020.05616.893.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C01

7c01


Resolution: 3.59→18.68 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 1137 4.73 %
Rwork0.2317 22894 -
obs0.2338 24031 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 340.38 Å2 / Biso mean: 162.9663 Å2 / Biso min: 75.46 Å2
Refinement stepCycle: final / Resolution: 3.59→18.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9297 0 0 0 9297
Num. residues----1215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.59-3.750.40381270.36728212948
3.75-3.950.35081280.314728522980
3.95-4.190.30461570.268528032960
4.19-4.510.27791340.214128602994
4.51-4.960.22611360.204428502986
4.96-5.660.25341740.219528413015
5.66-7.070.30581520.263528763028
7.07-18.680.25531290.194329913120
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)
14.1015-0.19122.71528.3906-0.62872.82911.6619-1.04860.216-0.6344-2.2467-1.68040.38680.38530.49330.9861-0.05230.31821.69150.10361.981776.258422.8058-12.8106
22.76882.12653.17555.94314.80944.6281-1.91591.18810.4688-0.31560.4528-0.9753-1.47910.64521.09661.6761-0.514-0.10571.5410.02062.306470.67732.6924-4.2309
34.39321.35991.66549.09930.38352.7033-0.00850.52580.2332-0.5936-0.1521-1.16410.60180.55910.12651.029-0.01740.14151.27980.1441.239459.381212.6579-15.3577
43.15912.05031.37268.29070.76463.84010.58051.12930.5382-0.07060.7605-0.85151.91071.34380.5160.1928-0.48230.49621.50120.40831.523864.124224.3681-16.3689
50.3147-0.6521-0.88215.50143.44466.4242-0.75920.62640.3363-0.17990.62390.7199-0.00880.73020.33411.1799-0.15190.01221.2410.10080.984434.261419.1345-31.6876
61.68630.41670.026.33970.23087.4426-0.2513-0.49020.0489-1.6718-0.05880.33671.4959-0.42690.25561.5337-0.0884-0.09771.12320.00420.96435.18199.158-32.9342
74.45430.12040.42423.6453-1.2712.5587-0.5490.0614-0.2995-0.33570.35850.1774-1.0896-0.7874-0.03211.18430.04160.07011.10260.04751.086628.923313.4405-27.7613
80.40060.1181-0.21643.8990.87620.63330.35390.3829-1.1367-0.9524-0.50190.81130.5522-0.98320.26641.2786-0.0802-0.69771.84450.31422.06331.0615-1.4594-24.4903
91.9720.14313.21370.17680.07225.59190.87031.188-1.8549-1.9295-0.2241-0.49690.7418-0.14410.50582.63160.0649-0.66932.1720.91112.297-9.50917.2094-27.4104
100.4877-1.05221.19574.13450.04644.48440.9222-0.38830.0965-2.3864-0.48511.01150.9849-0.0661-0.37082.13260.2635-0.78911.73170.05881.9124-0.20652.305-26.9453
116.28541.981-2.8956.0853-2.10798.90950.1757-0.3167-0.4049-0.1626-0.27220.0542-0.6016-0.05840.07750.80450.061-0.0760.9165-0.04160.784935.23647.5884-9.2758
129.4613-4.6516-2.33634.8004-0.69455.346-0.8388-0.41130.46260.51850.3875-1.03391.20420.03810.131.0719-0.0863-0.00410.9856-0.06581.126735.30596.6472-9.5861
138.81241.82921.24242.6641-0.90271.29531.21840.87790.4738-0.5925-0.56030.75610.6824-1.07390.57850.86910.13260.00731.08820.1881.066221.27653.3703-10.7794
145.86310.0069-2.28964.63370.3645.2182-0.1993-0.2711-0.3727-0.7139-0.08520.50131.0638-0.43330.17281.1385-0.0882-0.21741.25830.0271.34839.2595-8.5615-16.841
154.9805-5.8846-0.14866.75960.4065-0.06450.232-0.9501-0.7774-2.1361-0.7401-1.53392.66910.65010.61842.63830.56540.25051.67940.26581.123647.2885-8.8733-43.0157
164.74950.20621.66421.35861.7872.2194-0.32990.1238-2.06290.27171.5386-0.84650.51160.6001-1.51573.32170.8189-0.09341.5161-0.03851.965456.0034-15.8518-51.3947
171.0225-0.47390.03433.39270.97752.4147-0.52070.1554-0.3537-0.7740.23770.06391.13370.41580.20422.39650.13130.07351.1850.1081.020444.77463.9775-51.6313
185.8741-0.64040.4714.85561.70872.17820.0727-0.87010.09350.69930.24730.31960.8892-0.5545-0.6271.7696-0.14640.10531.34450.13681.157625.410415.8219-70.0114
191.7872-0.34951.54033.63520.05947.72380.36-0.5322-0.61870.27490.19080.49020.4105-0.548-0.60061.3813-0.25540.14281.15690.16761.225624.753919.7561-80.6649
202.8326-0.4880.14423.4251-0.98558.33180.1081-0.4642-0.8705-0.4254-0.15590.13360.1333-0.31430.2962.0418-0.31780.30861.39530.18921.430424.78318.7511-97.2094
217.94083.3654-2.32684.634-0.51778.713-0.0382-0.30910.47920.198-1.0786-0.07640.64931.97720.15231.46930.0631-0.02330.95220.34191.08747.254929.2972-69.2114
229.06682.1892-0.73318.0572-0.22432.38940.2581.4417-0.3692-0.7239-0.744-0.82110.3011.80.69391.37760.09520.25341.64250.06110.92743.856717.9545-71.899
235.97381.8917-3.24486.3430.37787.64330.64340.27280.53770.00810.0033-1.0664-0.08351.2020.40331.32420.04690.03421.58020.15851.181549.634524.1324-73.4538
243.44291.22411.39843.7572-4.86488.6919-0.323-0.0035-0.368-0.1707-0.0255-0.0321-1.37970.52130.44691.57150.2440.19960.7319-0.28021.116533.81128.3863-88.2302
256.6793-1.0351.7975.7243-3.42127.19990.6787-0.53630.18511.2913-0.44480.3487-1.3454-0.47470.38372.1617-0.29720.31081.2544-0.10991.137929.083637.5876-99.0322
263.8301-1.75152.767.1708-2.58128.72021.0462.5516-2.21060.5622-1.31621.31762.31872.3030.33161.6173-0.07740.27361.61930.01481.271328.956330.6849-99.8867
274.4581-1.43450.03086.9999-1.68068.0328-0.5476-0.82261.083-0.6146-0.70361.09290.0535-0.33410.35921.3433-0.3003-0.13711.248-0.14181.073429.261940.1649-107.6905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'R' and (resid 333 through 364 )R333 - 364
2X-RAY DIFFRACTION2chain 'R' and (resid 365 through 394 )R365 - 394
3X-RAY DIFFRACTION3chain 'R' and (resid 395 through 494 )R395 - 494
4X-RAY DIFFRACTION4chain 'R' and (resid 495 through 526 )R495 - 526
5X-RAY DIFFRACTION5chain 'L' and (resid 2 through 34 )L2 - 34
6X-RAY DIFFRACTION6chain 'L' and (resid 35 through 86 )L35 - 86
7X-RAY DIFFRACTION7chain 'L' and (resid 87 through 118 )L87 - 118
8X-RAY DIFFRACTION8chain 'L' and (resid 119 through 150 )L119 - 150
9X-RAY DIFFRACTION9chain 'L' and (resid 151 through 160 )L151 - 160
10X-RAY DIFFRACTION10chain 'L' and (resid 161 through 210 )L161 - 210
11X-RAY DIFFRACTION11chain 'H' and (resid 2 through 71 )H2 - 71
12X-RAY DIFFRACTION12chain 'H' and (resid 72 through 104 )H72 - 104
13X-RAY DIFFRACTION13chain 'H' and (resid 105 through 126 )H105 - 126
14X-RAY DIFFRACTION14chain 'H' and (resid 127 through 218 )H127 - 218
15X-RAY DIFFRACTION15chain 'A' and (resid 333 through 355 )A333 - 355
16X-RAY DIFFRACTION16chain 'A' and (resid 356 through 394 )A356 - 394
17X-RAY DIFFRACTION17chain 'A' and (resid 395 through 526 )A395 - 526
18X-RAY DIFFRACTION18chain 'B' and (resid 2 through 54 )B2 - 54
19X-RAY DIFFRACTION19chain 'B' and (resid 55 through 141 )B55 - 141
20X-RAY DIFFRACTION20chain 'B' and (resid 142 through 214 )B142 - 214
21X-RAY DIFFRACTION21chain 'C' and (resid 2 through 33 )C2 - 33
22X-RAY DIFFRACTION22chain 'C' and (resid 34 through 63 )C34 - 63
23X-RAY DIFFRACTION23chain 'C' and (resid 64 through 96 )C64 - 96
24X-RAY DIFFRACTION24chain 'C' and (resid 97 through 146 )C97 - 146
25X-RAY DIFFRACTION25chain 'C' and (resid 147 through 171 )C147 - 171
26X-RAY DIFFRACTION26chain 'C' and (resid 172 through 193 )C172 - 193
27X-RAY DIFFRACTION27chain 'C' and (resid 194 through 218 )C194 - 218

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