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- PDB-6ws6: Structural and functional analysis of a potent sarbecovirus neutr... -

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Entry
Database: PDB / ID: 6ws6
TitleStructural and functional analysis of a potent sarbecovirus neutralizing antibody
Components
  • S309 antigen-binding (Fab) fragment, heavy chain
  • S309 antigen-binding (Fab) fragment, light chain
KeywordsIMMUNE SYSTEM / fusion protein / neutralizing antibody / sarbecovirus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-JEF
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsPinto, D. / Park, Y.J. / Beltramello, M. / Walls, A.C. / Tortorici, M.A. / Bianchi, S. / Jaconi, S. / Culap, K. / Zatta, F. / Marco, A.D. ...Pinto, D. / Park, Y.J. / Beltramello, M. / Walls, A.C. / Tortorici, M.A. / Bianchi, S. / Jaconi, S. / Culap, K. / Zatta, F. / Marco, A.D. / Peter, A. / Guarino, B. / Spreafico, R. / Cameroni, E. / Case, J.B. / Chen, R.E. / Havenar-Daughton, C. / Snell, G. / Telenti, A. / Virgin, H.W. / Lanzavecchia, A. / Diamond, M.S. / Fink, K. / Veesler, D. / Corti, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
Citation
Journal: Nature / Year: 2020
Title: Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody.
Authors: Dora Pinto / Young-Jun Park / Martina Beltramello / Alexandra C Walls / M Alejandra Tortorici / Siro Bianchi / Stefano Jaconi / Katja Culap / Fabrizia Zatta / Anna De Marco / Alessia Peter / ...Authors: Dora Pinto / Young-Jun Park / Martina Beltramello / Alexandra C Walls / M Alejandra Tortorici / Siro Bianchi / Stefano Jaconi / Katja Culap / Fabrizia Zatta / Anna De Marco / Alessia Peter / Barbara Guarino / Roberto Spreafico / Elisabetta Cameroni / James Brett Case / Rita E Chen / Colin Havenar-Daughton / Gyorgy Snell / Amalio Telenti / Herbert W Virgin / Antonio Lanzavecchia / Michael S Diamond / Katja Fink / David Veesler / Davide Corti /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerged coronavirus that is responsible for the current pandemic of coronavirus disease 2019 (COVID-19), which has resulted in ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerged coronavirus that is responsible for the current pandemic of coronavirus disease 2019 (COVID-19), which has resulted in more than 3.7 million infections and 260,000 deaths as of 6 May 2020. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe several monoclonal antibodies that target the S glycoprotein of SARS-CoV-2, which we identified from memory B cells of an individual who was infected with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. One antibody (named S309) potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2, by engaging the receptor-binding domain of the S glycoprotein. Using cryo-electron microscopy and binding assays, we show that S309 recognizes an epitope containing a glycan that is conserved within the Sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails that include S309 in combination with other antibodies that we identified further enhanced SARS-CoV-2 neutralization, and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and antibody cocktails containing S309 for prophylaxis in individuals at a high risk of exposure or as a post-exposure therapy to limit or treat severe disease.
#1: Journal: bioRxiv / Year: 2020
Title: Structural and functional analysis of a potent sarbecovirus neutralizing antibody.
Authors: Dora Pinto / Young-Jun Park / Martina Beltramello / Alexandra C Walls / M Alejandra Tortorici / Siro Bianchi / Stefano Jaconi / Katja Culap / Fabrizia Zatta / Anna De Marco / Alessia Peter / ...Authors: Dora Pinto / Young-Jun Park / Martina Beltramello / Alexandra C Walls / M Alejandra Tortorici / Siro Bianchi / Stefano Jaconi / Katja Culap / Fabrizia Zatta / Anna De Marco / Alessia Peter / Barbara Guarino / Roberto Spreafico / Elisabetta Cameroni / James Brett Case / Rita E Chen / Colin Havenar-Daughton / Gyorgy Snell / Amalio Telenti / Herbert W Virgin / Antonio Lanzavecchia / Michael S Diamond / Katja Fink / David Veesler / Davide Corti
Abstract: SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than one million infections and 73,000 deaths . Vaccine and therapeutic discovery ...SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than one million infections and 73,000 deaths . Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S identified from memory B cells of a SARS survivor infected in 2003. One antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-binding domain. Using cryo-electron microscopy and binding assays, we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails including S309 along with other antibodies identified here further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease.
History
DepositionApr 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 19, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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

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Assembly

Deposited unit
A: S309 antigen-binding (Fab) fragment, heavy chain
B: S309 antigen-binding (Fab) fragment, light chain
C: S309 antigen-binding (Fab) fragment, heavy chain
D: S309 antigen-binding (Fab) fragment, light chain
E: S309 antigen-binding (Fab) fragment, heavy chain
F: S309 antigen-binding (Fab) fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9327
Polymers143,3356
Non-polymers5981
Water00
1
A: S309 antigen-binding (Fab) fragment, heavy chain
B: S309 antigen-binding (Fab) fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3763
Polymers47,7782
Non-polymers5981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: S309 antigen-binding (Fab) fragment, heavy chain
D: S309 antigen-binding (Fab) fragment, light chain


Theoretical massNumber of molelcules
Total (without water)47,7782
Polymers47,7782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: S309 antigen-binding (Fab) fragment, heavy chain
F: S309 antigen-binding (Fab) fragment, light chain


Theoretical massNumber of molelcules
Total (without water)47,7782
Polymers47,7782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.590, 132.590, 301.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody S309 antigen-binding (Fab) fragment, heavy chain


Mass: 24573.471 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody S309 antigen-binding (Fab) fragment, light chain


Mass: 23204.697 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
Has ligand of interestN
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: 4.62 Å3/Da / Density % sol: 73.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 1.1 M Sodium Malonate, 0.1 M HEPES, pH 7.0 and 0.5% (w/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9713 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2020
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9713 Å / Relative weight: 1
ReflectionResolution: 3.3→121.355 Å / Num. all: 41395 / Num. obs: 41395 / % possible obs: 100 % / Redundancy: 11.9 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.187 / Rsym value: 0.179 / Net I/av σ(I): 4.2 / Net I/σ(I): 13.2 / Num. measured all: 493741
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.3-3.48120.7517094459120.2250.7830.753.5100
3.48-3.6911.40.4911.66388556200.1510.5140.4915.2100
3.69-3.9412.30.3532.26506952800.1040.3680.3537.4100
3.94-4.2612.60.2263.46275549660.0660.2350.22611.5100
4.26-4.6711.90.1435.35424845650.0430.150.14316.7100
4.67-5.22120.1196.34997341680.0360.1250.11918.9100
5.22-6.0212.50.1216.34635637010.0350.1260.12118.3100
6.02-7.38110.1176.23498831700.0370.1230.11717.8100
7.38-10.4411.90.05711.32989525070.0170.060.05730.7100
10.44-93.75510.40.04912.81562815060.0160.0520.04929.999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.3 Å93.76 Å
Translation3.3 Å93.76 Å

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Processing

Software
NameVersionClassification
PHENIX1.18rc4-3812refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NB8

6nb8


Resolution: 3.3→93.76 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 2073 5.02 %
Rwork0.188 39218 -
obs0.1899 41291 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.28 Å2 / Biso mean: 77.9547 Å2 / Biso min: 31.3 Å2
Refinement stepCycle: final / Resolution: 3.3→93.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9630 0 41 0 9671
Biso mean--84.23 --
Num. residues----1297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3-3.380.25471220.232125782700
3.38-3.460.25561310.205725612692
3.46-3.550.23651250.198525672692
3.55-3.660.25151340.193325612695
3.66-3.780.22011380.200425862724
3.78-3.910.23251640.188625662730
3.91-4.070.21831100.173425982708
4.07-4.250.21661340.171725742708
4.25-4.480.1921550.15825842739
4.48-4.760.17581610.154325872748
4.76-5.130.2291070.164526502757
5.13-5.640.19351200.176526412761
5.64-6.460.2551430.212826542797
6.46-8.130.27491570.224726742831
8.14-93.760.24221720.202928373009
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)
18.18681.24941.0553.0352-0.2113.9306-0.11480.34990.1823-0.21220.00030.0956-0.02920.07850.11770.3894-0.0351-0.07760.3430.10410.3445.953620.057212.3663
24.14290.58840.20166.0023-3.3393.04480.010.1528-0.23790.28050.2713-0.54150.40880.1784-0.25810.55290.0577-0.19080.4525-0.1740.54135.426613.132934.439
35.5753-0.78553.7174.8175-2.49169.2742-0.1513-0.34540.22410.5247-0.0625-0.144-0.2504-0.69760.18920.3476-0.02880.04430.47850.02630.4368-1.648719.591733.3396
44.8492.5948-0.39382.4115-0.2842.8005-0.00460.1775-0.179-0.00040.1359-0.1647-0.01170.2005-0.12990.56510.0355-0.13230.3725-0.04510.470232.504825.190244.1387
53.4299-0.0901-1.28661.97290.15210.5592-0.0001-0.0466-0.14730.15680.00060.69130.4231-0.78510.03940.5167-0.28560.01440.94790.17870.7588-22.7259-2.558313.0305
61.81-0.71410.1991.7993-1.18721.1018-0.52070.0719-0.30610.95810.4170.6959-0.60030.09430.12381.0955-0.19590.19381.38890.26540.8621-31.2583-14.316943.065
73.2349-0.1976-1.56862.3387-0.6864.4851-0.0815-0.6436-0.26730.56880.02120.22270.9876-0.20140.0410.8483-0.1571-0.06460.64470.22020.6638-4.8649-14.495919.6446
81.97760.5829-0.16680.81210.04470.0476-0.43710.1589-0.37480.31650.24820.71660.382-0.19390.02851.417-0.61750.45061.62520.64271.0538-26.7127-30.125341.3729
94.59230.28642.33011.4943-0.4614.2209-0.2020.34970.1623-0.1040.1647-0.0603-0.17270.29680.01170.594-0.0053-0.10350.2813-0.04310.436444.740557.417654.5888
106.93270.5456-2.18492.6433-0.62465.9276-0.2989-0.21860.89250.10190.2540.7667-0.5578-0.48080.0370.52610.1162-0.11880.3909-0.05410.670110.209656.207445.7951
117.39872.05910.01011.78240.50032.80820.0773-0.3022-0.37060.37670.0706-0.1480.3715-0.2013-0.1460.81750.0141-0.17870.41250.03760.469436.272639.554565.0512
122.36761.0461.27882.0373-0.27725.5805-0.3521-0.03510.2029-0.01460.13290.0638-0.2696-0.2330.16370.39970.0631-0.09890.39950.04420.51779.503641.194841.1898
130.81061.9099-2.42946.9161-3.93578.60231.32030.1391-0.99080.0198-1.50720.07760.0512-0.73670.20480.7798-0.052-0.36261.16990.12060.5572-9.916112.8116-0.6371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 127 )A1 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 229 )A128 - 229
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 108 )B1 - 108
4X-RAY DIFFRACTION4chain 'B' and (resid 109 through 213 )B109 - 213
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 127 )C1 - 127
6X-RAY DIFFRACTION6chain 'C' and (resid 128 through 224 )C128 - 224
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 108)D1 - 108
8X-RAY DIFFRACTION8chain 'D' and (resid 109 through 208 )D109 - 208
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 127 )E1 - 127
10X-RAY DIFFRACTION10chain 'E' and (resid 128 through 229 )E128 - 229
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 108 )F1 - 108
12X-RAY DIFFRACTION12chain 'F' and (resid 109 through 213 )F109 - 213
13X-RAY DIFFRACTION13chain 'A' and (resid 401)A401

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