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- PDB-9sbb: Monoclonal Antibodies from COVID-19 Convalescent Patients Target ... -

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Basic information

Entry
Database: PDB / ID: 9sbb
TitleMonoclonal Antibodies from COVID-19 Convalescent Patients Target Cryptic Epitopes for Universal SARS-CoV-2 Neutralization
Components
  • (TAU-2310 Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / Immune complex / SARS-CoV-2 / receptor binding domain / neutralizing antibody
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 / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsDessau, M. / Harit, A.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation401/18 Israel
Israel Science Foundation352/23 Israel
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Monoclonal antibodies from COVID-19 convalescent patients target cryptic epitopes for broad SARS-CoV-2 neutralization.
Authors: Harit, A. / Mor, M. / Yefet, R. / Izhaki-Tavor, L.S. / Gal-Tanamy, M. / Freund, N.T. / Dessau, M.
History
DepositionAug 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2026Group: Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: TAU-2310 Fab Heavy Chain
L: TAU-2310 Fab Light Chain
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3189
Polymers71,7083
Non-polymers6116
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, assay for oligomerization, Bioloayer Interferometry (BLI)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-25 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.797, 87.975, 95.763
Angle α, β, γ (deg.)90.00, 108.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11R-762-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody TAU-2310 Fab Heavy Chain


Mass: 24084.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody TAU-2310 Fab Light Chain


Mass: 22906.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules R

#3: Protein Spike protein S1


Mass: 24716.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S, 2 / Cell (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 222 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Li / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium Citrate Tribasic Tetrahydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.12→60.42 Å / Num. obs: 49442 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.51 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.08232 / Rrim(I) all: 0.1544 / Net I/av σ(I): 7.52 / Net I/σ(I): 6.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRrim(I) all
2.12-2.161.6250.8427300.3720.737
2.37-2.450.67961880.5310.929
2.45-2.530.55760040.6330.762
2.53-2.630.43457980.7420.595

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Processing

Software
NameVersionClassification
PHENIXv1.21.2_5419refinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
TRUNCATEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→60.42 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 2449 4.95 %
Rwork0.1968 --
obs0.1988 49442 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→60.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 40 217 4995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114900
X-RAY DIFFRACTIONf_angle_d1.476675
X-RAY DIFFRACTIONf_dihedral_angle_d12.2991742
X-RAY DIFFRACTIONf_chiral_restr0.089737
X-RAY DIFFRACTIONf_plane_restr0.016856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.160.39881200.35272612X-RAY DIFFRACTION92
2.16-2.210.35931710.33912698X-RAY DIFFRACTION98
2.21-2.260.34161380.30872748X-RAY DIFFRACTION99
2.26-2.320.38131380.29112806X-RAY DIFFRACTION99
2.32-2.380.32211470.2852763X-RAY DIFFRACTION99
2.38-2.450.28961470.27612787X-RAY DIFFRACTION99
2.45-2.530.29961310.25882765X-RAY DIFFRACTION99
2.53-2.620.3011780.23682747X-RAY DIFFRACTION100
2.62-2.720.26271330.2342781X-RAY DIFFRACTION99
2.72-2.850.23651380.23332804X-RAY DIFFRACTION99
2.85-30.27071250.21582779X-RAY DIFFRACTION99
3-3.190.28371360.20322796X-RAY DIFFRACTION99
3.19-3.430.21431530.17622774X-RAY DIFFRACTION99
3.43-3.780.22041310.16762794X-RAY DIFFRACTION99
3.78-4.320.16621520.14122747X-RAY DIFFRACTION98
4.32-5.450.15351450.13222785X-RAY DIFFRACTION99
5.45-60.420.18031660.17092797X-RAY DIFFRACTION98
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)
13.19270.59890.24821.0614-0.64220.55040.2667-0.1028-0.7697-0.203-0.2054-0.12390.10130.019-0.25780.4535-0.0621-0.05040.2751-0.02470.44756.2591-9.008932.9497
23.03021.489-0.37752.04140.1732.2497-0.0092-0.2441-0.39310.2150.0511-0.28940.30240.1188-0.03110.3254-0.006-0.03520.2230.02970.326115.1549-2.779435.5416
31.98181.01930.16921.30330.15150.80030.0384-0.0183-0.17750.00630.0862-0.1085-0.01550.0219-0.10090.2671-0.0191-0.03830.22030.01950.24418.3518-1.401432.0185
40.71150.1608-0.46552.62-2.00634.1168-0.16060.83380.562-0.23930.1370.1305-0.8898-1.30270.06690.5250.1465-0.03720.77180.1790.4774-27.46043.75724.5256
51.3533-0.3104-0.37962.7577-0.80621.9633-0.01660.305-0.0435-0.37980.05710.0346-0.1851-0.38410.02990.3477-0.0112-0.0160.4035-0.0040.3607-18.6428-3.199824.6008
62.3698-0.04530.75462.3276-0.17932.78670.14310.48830.094-0.6894-0.01830.8619-0.0213-1.0188-0.12620.4680.0667-0.10850.74810.04840.5691-29.2574-2.8121.0493
72.2527-0.1143-0.30922.2471.0933.42530.13850.22550.12010.07740.1142-0.1467-0.00890.0839-0.31580.32950.0051-0.01420.24310.02820.22646.363416.598317.121
83.4263-0.08630.40751.7839-1.66361.5508-0.00930.2288-0.0413-0.0296-0.0498-0.0368-0.12090.04670.07110.3055-0.01790.01170.2437-0.02160.234714.550911.129819.5512
92.65820.3265-1.29580.9622-0.89042.45040.40860.34740.45040.20580.19820.3822-0.6413-0.6918-0.60270.45260.11150.08040.47180.10480.4046-16.726411.511721.9765
102.81031.1915-0.33132.7515-1.13792.13130.5382-0.00960.78770.41510.22420.3269-0.9997-0.4637-0.70640.60220.12440.17550.52310.05230.5367-17.508914.524526.8592
112.28420.47410.38732.2530.54643.4842-0.26150.8311-0.2587-0.64790.2844-0.15140.02020.4599-0.11240.4251-0.04750.03570.4903-0.0770.368737.475711.415617.5141
122.33750.24551.54131.74271.06861.7786-0.2591.2557-0.9867-0.63720.2131-0.59010.56460.5835-0.03410.65960.00010.20760.7706-0.26990.787844.8072-1.88915.8239
132.19640.4733-0.23072.40291.42122.7341-0.06610.1748-0.2059-0.15350.1492-0.2450.0420.1474-0.08790.18370.0121-0.02370.2649-0.00670.261540.200713.401631.5981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 83 )
3X-RAY DIFFRACTION3chain 'H' and (resid 84 through 130 )
4X-RAY DIFFRACTION4chain 'H' and (resid 131 through 154 )
5X-RAY DIFFRACTION5chain 'H' and (resid 155 through 188 )
6X-RAY DIFFRACTION6chain 'H' and (resid 189 through 224 )
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 23 )
8X-RAY DIFFRACTION8chain 'L' and (resid 24 through 105 )
9X-RAY DIFFRACTION9chain 'L' and (resid 106 through 155 )
10X-RAY DIFFRACTION10chain 'L' and (resid 156 through 213 )
11X-RAY DIFFRACTION11chain 'R' and (resid 334 through 358 )
12X-RAY DIFFRACTION12chain 'R' and (resid 359 through 393 )
13X-RAY DIFFRACTION13chain 'R' and (resid 394 through 527 )

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