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- EMDB-66856: Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66856
TitleOmicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain
Map data
Sample
  • Complex: BD58-0730-S 6P trimer complex
    • Protein or peptide: BD58-0730 heavy chain
    • Protein or peptide: BD58-0730 light chain
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / N-terminal domain / antibodies / N1/N2 loop / ACE2 competition / 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 / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / 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
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 ...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
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsLi ZQ / Niu X
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Emerg Microbes Infect / Year: 2024
Title: Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain.
Authors: Xiao Niu / Zhiqiang Li / Jing Wang / Fanchong Jian / Yuanling Yu / Weiliang Song / Ayijiang Yisimayi / Shuo Du / Zhiying Zhang / Qianran Wang / Jing Wang / Ran An / Yao Wang / Peng Wang / ...Authors: Xiao Niu / Zhiqiang Li / Jing Wang / Fanchong Jian / Yuanling Yu / Weiliang Song / Ayijiang Yisimayi / Shuo Du / Zhiying Zhang / Qianran Wang / Jing Wang / Ran An / Yao Wang / Peng Wang / Haiyan Sun / Lingling Yu / Sijie Yang / Tianhe Xiao / Qingqing Gu / Fei Shao / Youchun Wang / Junyu Xiao / Yunlong Cao /
Abstract: A multitude of functional mutations continue to emerge on the N-terminal domain (NTD) of the spike protein in SARS-CoV-2 Omicron subvariants. Understanding the immunogenicity of Omicron NTD and the ...A multitude of functional mutations continue to emerge on the N-terminal domain (NTD) of the spike protein in SARS-CoV-2 Omicron subvariants. Understanding the immunogenicity of Omicron NTD and the properties of antibodies elicited by it is crucial for comprehending the impact of NTD mutations on viral fitness and guiding vaccine design. In this study, we find that most of NTD-targeting antibodies isolated from individuals with BA.5/BF.7 breakthrough infection (BTI) are ancestral (wild-type or WT)-reactive and non-neutralizing. Surprisingly, we identified five ultra-potent neutralizing antibodies (NAbs) that can only bind to Omicron but not WT NTD. Structural analysis revealed that they bind to a unique epitope on the N1/N2 loop of NTD and interact with the receptor-binding domain (RBD) via the light chain. These Omicron-specific NAbs achieve neutralization through ACE2 competition and blockage of ACE2-mediated S1 shedding. However, BA.2.86 and BA.2.87.1, which carry insertions or deletions on the N1/N2 loop, can evade these antibodies. Together, we provided a detailed map of the NTD-targeting antibody repertoire in the post-Omicron era, demonstrating their vulnerability to NTD mutations enabled by its evolutionary flexibility, despite their potent neutralization. These results revealed the function of the indels in the NTD of BA.2.86/JN.1 sublineage in evading neutralizing antibodies and highlighted the importance of considering the immunogenicity of NTD in vaccine design.
History
DepositionOct 30, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66856.png

Downloads & links

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Map

FileDownload / File: emd_66856.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.413
Minimum - Maximum-2.0609517 - 3.0629096
Average (Standard dev.)0.0020809441 (±0.038490906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66856_msk_1.map
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Additional map: #1

Fileemd_66856_additional_1.map
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Half map: #2

Fileemd_66856_half_map_1.map
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Half map: #1

Fileemd_66856_half_map_2.map
Projections & Slices
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Sample components

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Entire : BD58-0730-S 6P trimer complex

EntireName: BD58-0730-S 6P trimer complex
Components
  • Complex: BD58-0730-S 6P trimer complex
    • Protein or peptide: BD58-0730 heavy chain
    • Protein or peptide: BD58-0730 light chain
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BD58-0730-S 6P trimer complex

SupramoleculeName: BD58-0730-S 6P trimer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BD58-0730 heavy chain

MacromoleculeName: BD58-0730 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.364939 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVQSGAEV KKPGASVKVS CKASGYTFTS YYMHWVRQAP GQGLEWMGII NPSGGSTSNA QKFQGRVTMT RDTFTSTVYM ELSSLRSED TAVYYCARDI ARGIGEYYFD YWGQGTLVTV SS

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Macromolecule #2: BD58-0730 light chain

MacromoleculeName: BD58-0730 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.718796 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQTASV SGSPGQSITI SCTGTSSDVG GYNYVSWYQQ HPGKAPKLMI YDVYKRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CSSYTTSSTL LFGGGTKLTV LGQ

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Macromolecule #3: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 32.433465 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CVNLITRTQS YTNSFTRGVY YPDKVFRSSV LHSTQDLFLP FFSNVTWFHA IHVSGTNGTK RFDNPALPFN DGVYFASTEK SNIIRGWIF GTTLDSKTQS LLIVNNATNV VIKVCEFQFC NDPFLDVYQK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKEGNF ...String:
CVNLITRTQS YTNSFTRGVY YPDKVFRSSV LHSTQDLFLP FFSNVTWFHA IHVSGTNGTK RFDNPALPFN DGVYFASTEK SNIIRGWIF GTTLDSKTQS LLIVNNATNV VIKVCEFQFC NDPFLDVYQK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKEGNF KNLREFVFKN IDGYFKIYSK HTPINLERDL PQGFSALEPL VDLPIGINIT RFQTLLALHR SYLTPGDSSS GW TAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTL

UniProtKB: Spike glycoprotein

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Macromolecule #4: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 25.110414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TESIVRFPNI TNLCPFHEVF NATTFASVYA WNRKRISNCV ADYSVIYNFA PFFAFKCYGV SPTKLNDLCF TNVYADSFVI RGNEVSQIA PGQTGNIADY NYKLPDDFTG CVIAWNSNKL DSKPSGNYNY LYRLFRKSKL KPFERDISTE IYQAGNKPCN G VAGPNCYS ...String:
TESIVRFPNI TNLCPFHEVF NATTFASVYA WNRKRISNCV ADYSVIYNFA PFFAFKCYGV SPTKLNDLCF TNVYADSFVI RGNEVSQIA PGQTGNIADY NYKLPDDFTG CVIAWNSNKL DSKPSGNYNY LYRLFRKSKL KPFERDISTE IYQAGNKPCN G VAGPNCYS PLQSYGFRPT YGVGHQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNG

UniProtKB: Spike glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 7 / 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

Concentration1.0 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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