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- EMDB-66903: SARS-CoV-2 Omicron JD.1.1 spike trimer (S-6P) in complex with 3 R... -

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Basic information

Entry
Database: EMDB / ID: EMD-66903
TitleSARS-CoV-2 Omicron JD.1.1 spike trimer (S-6P) in complex with 3 R102-9 Fabs and 3 C092 Fabs (3 RBD up)
Map data
Sample
  • Complex: SARS-CoV-2 Omicron JD.1.1 spike trimer (S-6P) in complex with 3 R102-9 Fabs and 3 C092 Fabs (3 RBD up)
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Heavy chain of C092 Fab
    • Protein or peptide: Light chain of C092 Fab
    • Protein or peptide: Heavy chain of R102-9 Fab
    • Protein or peptide: Light chain of R102-9 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike protein / Antibody Fab fragment / Complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion / positive regulation of viral entry into host cell / Initial triggering of complement / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsLiu B / Niu C / Li Z / Yuan H / Xiong X
Funding support China, 6 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82341085 China
Other governmentEKPG21-06
Other governmentSRPG22-002
Other government2023B1212060050
Other government2023B1212120009
Other governmentGIBHBRP24-02
CitationJournal: To be published
Title: Artificial intelligence-driven discovery of ultrapotent and broadly neutralizing antibodies against SARS-CoV-2 from a long-lived public antibody lineage
Authors: Yan Q / Huang X / Liu B / Yao Y / Zheng H / Song Y / Wu F / He Z / Chen F / Niu C / Li Z / Yuan H / Chen L / Zang N / Xiao J / Wang T / Chen C / Li S / Bai H / Li J / Wu M / Yao J / Zhao J / ...Authors: Yan Q / Huang X / Liu B / Yao Y / Zheng H / Song Y / Wu F / He Z / Chen F / Niu C / Li Z / Yuan H / Chen L / Zang N / Xiao J / Wang T / Chen C / Li S / Bai H / Li J / Wu M / Yao J / Zhao J / Yang Y / Zhu A / Xiong X / Zhao J
History
DepositionNov 2, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66903.png

Downloads & links

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Map

FileDownload / File: emd_66903.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 360 pix.
= 373.752 Å		1.04 Å/pix.
x 360 pix.
= 373.752 Å		1.04 Å/pix.
x 360 pix.
= 373.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0382 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0234
Minimum - Maximum-0.25696012 - 0.66700244
Average (Standard dev.)0.0011910702 (±0.014230383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 373.752 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66903_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66903_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 Omicron JD.1.1 spike trimer (S-6P) in complex with 3 R...

EntireName: SARS-CoV-2 Omicron JD.1.1 spike trimer (S-6P) in complex with 3 R102-9 Fabs and 3 C092 Fabs (3 RBD up)
Components
  • Complex: SARS-CoV-2 Omicron JD.1.1 spike trimer (S-6P) in complex with 3 R102-9 Fabs and 3 C092 Fabs (3 RBD up)
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Heavy chain of C092 Fab
    • Protein or peptide: Light chain of C092 Fab
    • Protein or peptide: Heavy chain of R102-9 Fab
    • Protein or peptide: Light chain of R102-9 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 Omicron JD.1.1 spike trimer (S-6P) in complex with 3 R...

SupramoleculeName: SARS-CoV-2 Omicron JD.1.1 spike trimer (S-6P) in complex with 3 R102-9 Fabs and 3 C092 Fabs (3 RBD up)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 138.187203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QCVNLITRTQ SYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AIHVSGTNGT KRFDNPALPF NDGVYFASTE KSNIIRGWI FGTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLDVYQ KNNKSWMESE FRVYSSANNC TFEYVSQPFL M DLEGKEGN ...String:
QCVNLITRTQ SYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AIHVSGTNGT KRFDNPALPF NDGVYFASTE KSNIIRGWI FGTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLDVYQ KNNKSWMESE FRVYSSANNC TFEYVSQPFL M DLEGKEGN FKNLREFVFK NIDGYFKIYS KHTPINLERD LPQGFSALEP LVDLPIGINI TRFQTLLALH RSYLTPVDSS SG WTAGAAA YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSNFRVQPTE SIVRFPNITN LCP FHEVFN ATTFASVYAW NRKRISNCVA DYSVIYNFAP FFAFKCYGVS PTKLNDLCFT NVYADSFVIR GNEVSQIAPG QTGN IADYN YKLPDDFTGC VIAWNSNKLD SKPSGNYNYL YRFLRKSKLK PFERDISTEI YQVGNKPCNG VAGPNCYSPL QSYGF RPTY GVGHQPYRVV VLSFELLHAP ATVCGPKKST NLVKNKCVNF NFNGLTGTGV LTESNKKFLP FQQFGRDIAD TTDAVR DPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQGVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEYVN NS YECDIPIGAG ICASYQTQTK SPRRARSVAS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVD C TMYICGDSTE CSNLLLQYGS FCTQLKRALT GIAVEQDKNT QEVFAQVKQI YKTPPIKYFG GFNFSQILPD PSKPSKRSP IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICAQKFNG LTVLPPLLTD EMIAQYTSAL LAGTITSGWT FGAGPALQIP FPMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLSSTPSALG KLQDVVNHNA QALNTLVKQL SSKFGAISSV L NDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS AP HGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRNFYEPQI ITTDNTFVSG NCDVVIGIVN NTV YDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESLIDLQEL GKYEQYIKGS GREN LYFQG GGGSGYIPEA PRDGQAYVRK DGEWVLLSTF LGHHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #2: Heavy chain of C092 Fab

MacromoleculeName: Heavy chain of C092 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.114055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGSFT NHFISWVRQA PGQGLEWMGR IIPILGTANY AQNFQGRVMM TADKSTSTAY MELSSLRSE DTAVYYCARD SGYSGYGSTY YMDVWGKGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGSFT NHFISWVRQA PGQGLEWMGR IIPILGTANY AQNFQGRVMM TADKSTSTAY MELSSLRSE DTAVYYCARD SGYSGYGSTY YMDVWGKGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD

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Macromolecule #3: Light chain of C092 Fab

MacromoleculeName: Light chain of C092 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.886127 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SGAPGQRVTI SCTGSNSNIG AGYDVHWYQQ LPGAAPKLLI YGNNNRPSGV PDRFSGSKSD TSASLAITGL QVEDEADYY CQSYDSSLSD SVFGSGTKVT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSVLTQPPSV SGAPGQRVTI SCTGSNSNIG AGYDVHWYQQ LPGAAPKLLI YGNNNRPSGV PDRFSGSKSD TSASLAITGL QVEDEADYY CQSYDSSLSD SVFGSGTKVT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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Macromolecule #4: Heavy chain of R102-9 Fab

MacromoleculeName: Heavy chain of R102-9 Fab / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.422412 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGIIVS RNYMSWVRQA PGKRPEWVSL IYPGGSTFYA DSVKGRFTIS RDNSKNMLFL QMNSLRAED TAVYYCARDL TIRGEASWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
EVQLVESGGG LVQPGGSLRL SCAASGIIVS RNYMSWVRQA PGKRPEWVSL IYPGGSTFYA DSVKGRFTIS RDNSKNMLFL QMNSLRAED TAVYYCARDL TIRGEASWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCD

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Macromolecule #5: Light chain of R102-9 Fab

MacromoleculeName: Light chain of R102-9 Fab / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.547113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQSPAT LSVSPGERAT LSCRASQSFN SNLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYGDWPLWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPAT LSVSPGERAT LSCRASQSFN SNLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYGDWPLWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 18 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
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:

8hc4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 206030
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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