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

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Basic information

Entry
Database: PDB / ID: 9sat
TitleMonoclonal Antibodies from COVID-19 Convalescent Patients Target Cryptic Epitopes for Universal SARS-CoV-2 Neutralization
Components
  • Spike protein S1
  • TAU-1109 Fab Heavy Chain
  • TAU-1109 Fab Light Chain
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
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 1, 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-1109 Fab Heavy Chain
L: TAU-1109 Fab Light Chain
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3666
Polymers77,1703
Non-polymers1963
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, assay for oligomerization, Biolayer Interferometry (BLI)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-115 kcal/mol
Surface area27450 Å2
Unit cell
Length a, b, c (Å)83.264, 102.996, 225.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11L-301-

ZN

21L-408-

HOH

31L-448-

HOH

41L-475-

HOH

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Components

#1: Antibody TAU-1109 Fab Heavy Chain


Mass: 24067.857 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-1109 Fab Light Chain


Mass: 23679.363 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)
#3: Protein Spike protein S1


Mass: 29422.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P0DTC2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Zinc Acetate Dehydrate, 0.1M Sodium Cacodylate Trihydrate, 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8371 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8371 Å / Relative weight: 1
ReflectionResolution: 2.56→93.69 Å / Num. obs: 28734 / % possible obs: 90.72 % / Redundancy: 1.9 % / Biso Wilson estimate: 21.78 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.0671 / Rpim(I) all: 0.0671 / Rrim(I) all: 0.0949 / Net I/σ(I): 9.39
Reflection shellResolution: 2.56→2.65 Å / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.65 / Num. unique obs: 2658 / CC1/2: 0.838 / CC star: 0.955 / Rpim(I) all: 0.232 / Rrim(I) all: 0.328 / % possible all: 85.56

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Processing

Software
NameVersionClassification
PHENIXv1.21refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
TRUNCATEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→93.69 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 1416 4.93 %RANDOM
Rwork0.2309 ---
obs0.2331 28734 90.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→93.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 3 252 5095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014968
X-RAY DIFFRACTIONf_angle_d1.4556770
X-RAY DIFFRACTIONf_dihedral_angle_d14.7981776
X-RAY DIFFRACTIONf_chiral_restr0.078746
X-RAY DIFFRACTIONf_plane_restr0.02877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.650.35971420.28812516X-RAY DIFFRACTION86
2.65-2.760.33181330.28272143X-RAY DIFFRACTION72
2.76-2.880.29691310.27512874X-RAY DIFFRACTION96
2.88-3.040.31911470.26852935X-RAY DIFFRACTION98
3.04-3.230.33161550.2622930X-RAY DIFFRACTION99
3.23-3.480.32891110.24812624X-RAY DIFFRACTION87
3.48-3.830.25511350.21742663X-RAY DIFFRACTION88
3.83-4.380.23141370.1932660X-RAY DIFFRACTION88
4.38-5.520.19841560.17212940X-RAY DIFFRACTION96
5.52-93.690.25941690.22163031X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 61.8081 Å / Origin y: 32.3404 Å / Origin z: 83.4138 Å
111213212223313233
T0.0082 Å2-0.0322 Å2-0.0549 Å2-0.0216 Å20.0256 Å2--0.0085 Å2
L0.0044 °20.004 °20.0212 °2-0.0017 °2-0.005 °2--0.0044 °2
S-0.0436 Å °0.0077 Å °-0.0092 Å °0.0056 Å °-0.0141 Å °0.0102 Å °-0.01 Å °0.0161 Å °-0 Å °
Refinement TLS groupSelection details: all

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