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- EMDB-51901: SARS-CoV-2 S protein in complex with pT1679 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-51901
TitleSARS-CoV-2 S protein in complex with pT1679 Fab
Map data
Sample
  • Complex: 3:3 pT1679 Fab-Spike complex
    • Complex: pT1679 Fab
      • Protein or peptide: pT1679 Fab heavy chain
      • Protein or peptide: pT1679 Fab light chain
    • Complex: Spike protein S1
      • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / PROTEIN BINDING
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 / entry receptor-mediated virion attachment to host cell / membrane fusion / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 / Tequatrovirus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsHansen G / Benecke T / Vollmer B / Gruenewald K / Krey T
Funding support Germany, 9 items
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, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51901.png

Downloads & links

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Map

FileDownload / File: emd_51901.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 311 pix.
= 211.48 Å		0.68 Å/pix.
x 318 pix.
= 216.24 Å		0.68 Å/pix.
x 273 pix.
= 185.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-3.4999087 - 5.5692635
Average (Standard dev.)0.003997595 (±0.09139985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin14021990
Dimensions318273311
Spacing273318311
CellA: 185.64 Å / B: 216.24 Å / C: 211.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51901_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51901_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 3:3 pT1679 Fab-Spike complex

EntireName: 3:3 pT1679 Fab-Spike complex
Components
  • Complex: 3:3 pT1679 Fab-Spike complex
    • Complex: pT1679 Fab
      • Protein or peptide: pT1679 Fab heavy chain
      • Protein or peptide: pT1679 Fab light chain
    • Complex: Spike protein S1
      • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 3:3 pT1679 Fab-Spike complex

SupramoleculeName: 3:3 pT1679 Fab-Spike complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: pT1679 Fab

SupramoleculeName: pT1679 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Spike protein S1

SupramoleculeName: Spike protein S1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 140.735234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP F LMDLEGKQ ...String:
VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP F LMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINLV RDLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SS SGWTAGA AAYYVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TESIVRFPNI TNL CPFGEV FNATRFASVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQT GKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSY GFQP TNGVGYQPYR VVVLSFELLH APATVCGPDK STNLVKNKCV NFNFNGLTGT GVLTESNKKF LPFQQFGRDI ADTTDA VRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQDVNCT EVPVAIHADQ LTPTWRVYST GSNVFQTRAG CLIGAEH VN NSYECDIPIG AGICASYQTQ TNSPGSASSV ASQSIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTEIL PVSMTKTS V DCTMYICGDS TECSNLLLQY GSFCTQLNRA LTGIAVEQDK NTQEVFAQVK QIYKTPPIKD FGGFNFSQIL PDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNQ NAQALNTLVK QLSSNFGAIS S VLNDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QS APHGVVF LHVTYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGNCDVVIGI VNN TVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGKYEQGSG YIPE APRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEK

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #2: pT1679 Fab heavy chain

MacromoleculeName: pT1679 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.693107 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MKLCILLAVV AFVGLSLGQV QLVQSGAEVK KPGSSVKVSC RASGGTFSSY AISWVRQAPG QGLEWMGTII PVFGAPDYAQ KFQGRVTIT ADESTSTAYM EVRSLRSEDT AVYYCARDAS PYYYDRSGYP RWAEDLHHWG QGTMVTVSSA STKGPSVFPL A PSSKSTSG ...String:
MKLCILLAVV AFVGLSLGQV QLVQSGAEVK KPGSSVKVSC RASGGTFSSY AISWVRQAPG QGLEWMGTII PVFGAPDYAQ KFQGRVTIT ADESTSTAYM EVRSLRSEDT AVYYCARDAS PYYYDRSGYP RWAEDLHHWG QGTMVTVSSA STKGPSVFPL A PSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NT KVDKRVE PKSCDKTDDD DK

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Macromolecule #3: pT1679 Fab light chain

MacromoleculeName: pT1679 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.872146 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: ASQSVLTQPP SVSGAPGQRV TISCTGSSSN IGAGYDVHWY QQLPGTAPKL LIYGNSNRPS GVPDRFSGSK SGTSGSLAIS GLQPEDEAD YYCQSYDSSL SGSIFGGGTK LTVLGQPKAA PSVTLFPPSS EELQANKATL VCLISDFYPG AVTVAWKADS S PVKAGVET ...String:
ASQSVLTQPP SVSGAPGQRV TISCTGSSSN IGAGYDVHWY QQLPGTAPKL LIYGNSNRPS GVPDRFSGSK SGTSGSLAIS GLQPEDEAD YYCQSYDSSL SGSIFGGGTK LTVLGQPKAA PSVTLFPPSS EELQANKATL VCLISDFYPG AVTVAWKADS S PVKAGVET TTPSKQSNNK YAASSYLSLT PEQWKSHRSY SCQVTHEGST VEKTVAPTEC S

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.34 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xkl

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 454108
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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