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- PDB-7tcq: Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in comp... -

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Basic information

Entry
Database: PDB / ID: 7tcq
TitleCrystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide
Components
  • (Anti-SARS-CoV-2 antibody WS6 Fab light ...) x 2
  • Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
  • Pegylated spike S2 peptide
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / spike / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Spike glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsZhou, T. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Structure / Year: 2022
Title: Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability.
Authors: Shi, W. / Wang, L. / Zhou, T. / Sastry, M. / Yang, E.S. / Zhang, Y. / Chen, M. / Chen, X. / Choe, M. / Creanga, A. / Leung, K. / Olia, A.S. / Pegu, A. / Rawi, R. / Schon, A. / Shen, C.H. / ...Authors: Shi, W. / Wang, L. / Zhou, T. / Sastry, M. / Yang, E.S. / Zhang, Y. / Chen, M. / Chen, X. / Choe, M. / Creanga, A. / Leung, K. / Olia, A.S. / Pegu, A. / Rawi, R. / Schon, A. / Shen, C.H. / Stancofski, E.D. / Talana, C.A. / Teng, I.T. / Wang, S. / Corbett, K.S. / Tsybovsky, Y. / Mascola, J.R. / Kwong, P.D.
History
DepositionDec 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
L: Anti-SARS-CoV-2 antibody WS6 Fab light chain
C: Pegylated spike S2 peptide
A: Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
B: Anti-SARS-CoV-2 antibody WS6 Fab light chain
D: Pegylated spike S2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,94328
Polymers95,8096
Non-polymers2,13422
Water13,241735
1
H: Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
L: Anti-SARS-CoV-2 antibody WS6 Fab light chain
C: Pegylated spike S2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,16516
Polymers47,8963
Non-polymers1,26913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
B: Anti-SARS-CoV-2 antibody WS6 Fab light chain
D: Pegylated spike S2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,77812
Polymers47,9133
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.063, 64.518, 137.963
Angle α, β, γ (deg.)90.000, 117.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-569-

HOH

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Components

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Pegylated spike S2 peptide


Mass: 1462.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: N-term acetylated and C-term pegylated
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Antibody , 3 types, 4 molecules HALB

#1: Antibody Anti-SARS-CoV-2 antibody WS6 Fab heavy chain


Mass: 23120.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody Anti-SARS-CoV-2 antibody WS6 Fab light chain


Mass: 23312.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK 293F / Production host: Homo sapiens (human)
#4: Antibody Anti-SARS-CoV-2 antibody WS6 Fab light chain


Mass: 23329.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK 293F / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 757 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY
Sequence details(I2J) at the carboxy-terminus of the peptide (chains C and D) is a pegylation. The amino-terminal ...(I2J) at the carboxy-terminus of the peptide (chains C and D) is a pegylation. The amino-terminal glutamine of one of the light chains in the asymmetric unit (chain L) spontaneously formed pyroglutamate.

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M Ammonium sulfate and 30 % PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 75544 / % possible obs: 95.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.88 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.083 / Rrim(I) all: 0.157 / Χ2: 1.453 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.03-2.072.80.79233260.4130.5130.9490.49288.8
2.07-2.12.90.70234680.5290.4580.8440.52591.4
2.1-2.1430.63434950.570.4090.760.57793.6
2.14-2.193.10.58936130.5970.380.7050.62594.6
2.19-2.233.10.56935560.5740.3710.6830.62795.3
2.23-2.293.20.50736210.6270.3310.610.6796
2.29-2.343.20.46636360.6480.3040.560.67596.1
2.34-2.413.30.4536530.6890.2930.540.7396.8
2.41-2.483.30.39636740.7470.2580.4750.80896.7
2.48-2.563.20.34734590.7830.2270.4170.90790.8
2.56-2.653.50.31636820.8220.1970.3740.97697.4
2.65-2.763.60.25937080.8630.160.3061.10798.1
2.76-2.883.60.21137060.9180.1290.2481.29198.1
2.88-3.033.60.1737300.9380.1050.2011.51898
3.03-3.223.50.13237350.9640.0820.1561.99597.9
3.22-3.473.40.10536870.9780.0660.1252.37397.2
3.47-3.823.30.08735220.9840.0550.1032.94192.2
3.82-4.373.60.0737240.990.0430.0822.91997
4.37-5.513.60.0637150.9920.0370.0712.8996.5
5.51-503.50.05837690.9930.0350.0682.92195.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.8 Å40.23 Å
Translation3.8 Å40.23 Å

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JKT

7jkt


Resolution: 2.02→40.23 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 1989 2.63 %
Rwork0.1715 73555 -
obs0.1725 75544 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.1 Å2 / Biso mean: 32.9514 Å2 / Biso min: 12.88 Å2
Refinement stepCycle: final / Resolution: 2.02→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 148 735 7603
Biso mean--53.7 38.92 -
Num. residues----873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087005
X-RAY DIFFRACTIONf_angle_d0.9289553
X-RAY DIFFRACTIONf_dihedral_angle_d7.011967
X-RAY DIFFRACTIONf_chiral_restr0.0571052
X-RAY DIFFRACTIONf_plane_restr0.0071193
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 (%)
2.02-2.070.27631130.24674152426575
2.07-2.130.25921340.22645066520092
2.13-2.190.24791400.20415167530794
2.19-2.260.26141450.1975328547396
2.26-2.340.24921440.19745370551497
2.34-2.430.24171440.19665320546497
2.43-2.540.22941450.19665349549496
2.54-2.680.27041400.19075171531194
2.68-2.850.21711470.18325429557698
2.85-3.070.20691490.16965477562698
3.07-3.370.2091480.16145461560998
3.37-3.860.18391420.14745245538794
3.86-4.860.1751480.13635483563198
4.86-40.230.20181500.16875537568796
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)
11.6988-0.80430.14244.96530.37712.21350.0013-0.06030.06880.1063-0.01950.0550.170.03530.02130.1101-0.0011-0.01520.1569-0.01930.134542.19312.692221.1952
24.20110.64021.20011.91340.76552.1307-0.0565-0.05890.0426-0.0338-0.01440.11850.011-0.24330.05470.1120.01370.01360.14080.01760.168112.989619.42318.2319
33.4159-0.35160.3481.62690.38471.7502-0.00670.143-0.0212-0.0818-0.06390.25330.0469-0.24710.05590.13710.0045-0.01750.152-0.03730.199735.0931-7.31481.021
41.7619-1.4588-0.29931.2101-0.0906-0.0219-0.02040.1785-0.22540.0596-0.01330.22220.0238-0.02280.01330.12040.0012-0.01250.1975-0.03040.202423.02058.84384.9945
51.28520.4054-0.23026.55291.15031.9488-0.13050.18020.0691-0.4060.3077-0.3753-0.22820.1049-0.15250.16740.0134-0.01510.25720.03340.242116.601925.3308-2.7412
61.7845-0.37270.6316.00492.49863.0919-0.0580.15970.06880.0098-0.05780.3023-0.2439-0.13670.11480.1013-0.01070.040.22450.05510.174512.389123.87892.569
77.38742.954-0.50877.1376-2.43181.90820.1713-0.234-0.7890.1925-0.0327-0.65581.32360.6854-0.13820.3720.1646-0.05930.295-0.03570.264351.1296-11.793615.8213
88.08843.9884-5.472.6473-3.01075.09320.132-0.0803-0.32380.0739-0.1795-0.18020.23470.19280.05670.37090.0866-0.08620.2559-0.06510.1947-15.800230.316338.5199
95.04262.18150.20124.12411.25493.8140.15520.19380.3646-0.2241-0.08460.04650.04310.0491-0.08240.20370.0917-0.00820.1750.01030.1494-20.299238.987939.1867
104.0870.5101-2.25861.2738-0.39953.25120.07430.05920.3216-0.01320.02530.07710.11780.1356-0.09950.25790.0719-0.03750.2502-0.03690.2043-12.60638.067741.6947
111.8126-0.0325-1.06761.8217-0.47872.8993-0.15470.0440.35870.1444-0.1218-0.3266-0.1480.48390.22670.20710.02430.00750.1911-0.0140.220918.630132.935135.7864
124.7857-1.53982.59581.9294-1.23725.2308-0.0135-0.1652-0.11640.2137-0.01010.0904-0.0684-0.13340.03170.18670.02060.03490.16960.03720.162215.569428.485540.1431
134.10890.59880.91362.52240.51863.28890.0925-0.55020.07910.1568-0.12290.08510.3230.16530.08940.2882-0.00880.0160.3608-0.10130.1778-10.973541.620362.0241
143.5768-0.3402-0.35690.23670.09330.5749-0.1947-0.46930.33810.05060.0832-0.0167-0.03420.110.05190.33180.0055-0.03040.1863-0.02430.234713.306242.17749.0085
154.71640.2056-2.28181.43020.00564.51970.0049-0.25190.5522-0.00680.0325-0.1291-0.76690.2549-0.0460.4148-0.0136-0.09470.20810.00520.300524.094642.320646.0365
168.6112-1.76293.00663.2977-4.78877.03090.459-0.6381-0.22530.20710.06070.78960.194-0.9822-0.48950.3533-0.010.01710.3605-0.05770.2618-30.850139.569150.5126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-IDBeg PDB ins code
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 111 )H1 - 111
2X-RAY DIFFRACTION2chain 'H' and (resid 112 through 213 )H112 - 213
3X-RAY DIFFRACTION3chain 'L' and (resid 2 through 75 )L2 - 75
4X-RAY DIFFRACTION4chain 'L' and (resid 76 through 139 )L76 - 139
5X-RAY DIFFRACTION5chain 'L' and (resid 140 through 158 )L140 - 158
6X-RAY DIFFRACTION6chain 'L' and (resid 159 through 213 )L159 - 213
7X-RAY DIFFRACTION7chain 'C' and (resid 1149 through 1157 )C1149 - 1157
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 32 )A1 - 32
9X-RAY DIFFRACTION9chain 'A' and (resid 33 through 82 )A33 - 82
10X-RAY DIFFRACTION10chain 'A' and (resid 82A through 111 )A82 - 111A
11X-RAY DIFFRACTION11chain 'A' and (resid 112 through 134 )A112 - 134
12X-RAY DIFFRACTION12chain 'A' and (resid 135 through 213 )A135 - 213
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 89 )B1 - 89
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 155 )B90 - 155
15X-RAY DIFFRACTION15chain 'B' and (resid 156 through 213 )B156 - 213
16X-RAY DIFFRACTION16chain 'D' and (resid 1149 through 1157 )D1149 - 1157

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