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- PDB-9h6u: SARS-CoV-2 S protein in complex with pT1679 Fab -

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Basic information

Entry
Database: PDB / ID: 9h6u
TitleSARS-CoV-2 S protein in complex with pT1679 Fab
Components
  • Spike glycoprotein,Fibritin
  • pT1679 Fab heavy chain
  • pT1679 Fab light chain
KeywordsPROTEIN BINDING / PROTEIN BINDING/IMMUNE SYSTEM
Function / homology
Function and homology information


virion component / 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 ...virion component / 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
Fibritin C-terminal / Fibritin C-terminal region / 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. ...Fibritin C-terminal / Fibritin C-terminal region / 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
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Tequatrovirus T4
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsHansen, G. / Benecke, T. / Vollmer, B. / Gruenewald, K. / Krey, T.
Funding support Germany, 9items
OrganizationGrant numberCountry
Other government14-76103-184 CORONA-12/20
Other government14-76103-184 CORONA-15/20
German Federal Ministry for Education and ResearchCOVIM (FKZ: 01KX2021) Germany
German Federal Ministry for Education and ResearchRAPID (FKZ: 01KI1723G) Germany
German Research Foundation (DFG)EXC 2155 Germany
German Research Foundation (DFG)2485 VIPER (398066876/GRK 2485/1) Germany
Other government14-76403-184
Other government14-76103-184
Other governmentMWK TiHO SARS-COV-2
CitationJournal: mBio / Year: 2025
Title: A critical residue in a conserved RBD epitope determines neutralization breadth of pan-sarbecovirus antibodies with recurring YYDRxxG motifs.
Authors: Saskia C Stein / George Ssebyatika / Tim Benecke / Luisa Ströh / Manoj K Rajak / Benjamin Vollmer / Sarah Menz / Ja-Yun Waldmann / Sarah N Tipp / Okechukwu Ochulor / Elisabeth Herold / ...Authors: Saskia C Stein / George Ssebyatika / Tim Benecke / Luisa Ströh / Manoj K Rajak / Benjamin Vollmer / Sarah Menz / Ja-Yun Waldmann / Sarah N Tipp / Okechukwu Ochulor / Elisabeth Herold / Britta Schwarzloh / Doris Mutschall / Jasmin Zischke / Talia Schneider / Imke Hinrichs / Rainer Blasczyk / Hannah Kleine-Weber / Markus Hoffmann / Florian Klein / Franziska K Kaiser / Mariana Gonzalez-Hernandez / Federico Armando / Malgorzata Ciurkiewicz / Georg Beythien / Stefan Pöhlmann / Wolfgang Baumgärtner / Kay Gruenewald / Albert Osterhaus / Thomas F Schulz / Thomas Krey / Guido Hansen /
Abstract: The emergence of pandemic coronaviruses remains a global health concern, highlighting the need for broadly neutralizing antibodies (bnAbs) that can target multiple sarbecoviruses. In this study, we ...The emergence of pandemic coronaviruses remains a global health concern, highlighting the need for broadly neutralizing antibodies (bnAbs) that can target multiple sarbecoviruses. In this study, we isolated and characterized a novel antibody, pT1679, that demonstrates exceptional neutralization breadth. The antibody prevented infection with SARS-CoV-2 variants of concern, such as Omicron BA.1, and effectively neutralized pseudotyped viruses displaying S proteins from many SARS-CoV-2 variants and various bat and pangolin sarbecoviruses, including both SARS-CoV-like and SARS-CoV-2-like viruses. In addition, pT1679 reduced the viral load in the lung of infected Syrian hamsters and prevented the severe lung pathology typical for SARS-CoV-2 infections. The cryo-electron microscopy structure of pT1679 in complex with SARS-CoV-2 S revealed that the antibody employs a YYDRxxG motif to recognize a highly conserved epitope on the RBD. Through detailed structural analysis, mutagenesis studies, and binding assays, we identified RBD residue 384 as a critical determinant of antibody recognition. Structure-function analyses of several related bnAbs, such as COVA1-16, allowed for the classification of YYDRxxG antibodies into two distinct groups that differ in neutralization breadth. Our findings provide crucial insights into the molecular basis of broad neutralization and offer strategic guidance for selecting therapeutic antibodies in preparation for future outbreaks.IMPORTANCEThe threat of emerging coronaviruses demands therapeutic strategies capable of targeting both current and future circulating viruses. We report the discovery and characterization of pT1679, a broadly neutralizing antibody that demonstrates cross-reactivity against diverse sarbecoviruses, including SARS-CoV, SARS-CoV-2 variants, and related viruses from bats and pangolins. pT1679 targets a highly conserved epitope via a YYDRxxG motif in the paratope, with RBD residue 384 serving as a critical determinant of recognition. Our analysis allows for a classification of YYDRxxG antibodies, providing a framework for predicting antibody effectiveness against emerging sarbecoviruses.
History
DepositionOct 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Sep 24, 2025Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein,Fibritin
H: pT1679 Fab heavy chain
L: pT1679 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,5224
Polymers191,3003
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Spike glycoprotein,Fibritin / S glycoprotein / E2 / Peplomer protein / Collar protein / Whisker antigen control protein


Mass: 140735.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2, (gene. exp.) Tequatrovirus T4
Gene: S, 2, wac / Cell line (production host): HEK293ExPi / Production host: Homo sapiens (human) / References: UniProt: P0DTC2, UniProt: P10104
#2: Antibody pT1679 Fab heavy chain


Mass: 27693.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody pT1679 Fab light chain


Mass: 22872.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#4: 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
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
13:3 pT1679 Fab-Spike complexCOMPLEX#1-#30RECOMBINANT
2pT1679 FabCOMPLEX#2-#31RECOMBINANT
3Spike protein S1COMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Severe acute respiratory syndrome coronavirus 22697049
33Enterobacteria phage T4 (virus)10665
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Drosophila melanogaster (fruit fly)7227S2
43Homo sapiens (human)9606HEK293ExPi
Buffer solutionpH: 7.4
SpecimenConc.: 0.34 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 454108 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033438
ELECTRON MICROSCOPYf_angle_d0.4874678
ELECTRON MICROSCOPYf_dihedral_angle_d3.631487
ELECTRON MICROSCOPYf_chiral_restr0.043497
ELECTRON MICROSCOPYf_plane_restr0.008611

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