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- EMDB-62925: Locally refined region of SARS-CoV-2 spike in complex with antibo... -

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Basic information

Entry
Database: EMDB / ID: EMD-62925
TitleLocally refined region of SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2.
Map data
Sample
  • Complex: SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2
    • Complex: The Fab of 3E2
      • Protein or peptide: Light chain of 3E2
      • Protein or peptide: Heavy chain of 3E2
    • Complex: SARS-CoV-2 spike
      • Protein or peptide: Spike protein S1
    • Complex: The Fab of 9G11
      • Protein or peptide: Light chain of 9G11
      • Protein or peptide: Heavy chain of 9G11
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / RBD / Fab / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / 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 ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / 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 / 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, 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 ...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
Biological speciesMus musculus (house mouse) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsJiang Y / Sun H / Zheng Q / Li S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Emerg Microbes Infect / Year: 2024
Title: Structural insight into broadening SARS-CoV-2 neutralization by an antibody cocktail harbouring both NTD and RBD potent antibodies.
Authors: Wenling Jiang / Yanan Jiang / Hui Sun / Tingting Deng / Kunyu Yu / Qianjiao Fang / Huimin Ge / Miaoling Lan / Yanling Lin / Zhongyue Fang / Yali Zhang / Lizhi Zhou / Tingting Li / Hai Yu / ...Authors: Wenling Jiang / Yanan Jiang / Hui Sun / Tingting Deng / Kunyu Yu / Qianjiao Fang / Huimin Ge / Miaoling Lan / Yanling Lin / Zhongyue Fang / Yali Zhang / Lizhi Zhou / Tingting Li / Hai Yu / Qingbing Zheng / Shaowei Li / Ningshao Xia / Ying Gu /
Abstract: The continual emergence of highly pathogenic novel coronaviruses and their variants has underscored the importance of neutralizing monoclonal antibodies (mAbs) as a pivotal therapeutic approach. In ...The continual emergence of highly pathogenic novel coronaviruses and their variants has underscored the importance of neutralizing monoclonal antibodies (mAbs) as a pivotal therapeutic approach. In the present study, we report the specific neutralizing antibodies 13H7 and 9G11, which target the N-terminal domain (NTD) and receptor-binding domain (RBD) of the SARS-CoV-2, respectively. The comparative analysis observed that 13H7 not only neutralizes early variants of concern (VOCs) but also exhibits neutralizing activity against the Omicron sublineage, including BA.4, BA.5, BQ.1, and BQ.1.1. 9G11, as an RBD antibody, also demonstrated remarkable neutralizing efficacy. A cocktail antibody combining 13H7 and 9G11 with the previously reported 3E2 broaden the neutralization spectrum against new variants of the SARS-CoV-2. We elucidated the cryo-EM structure of the complex, clarifying the mechanism of action of the cocktail antibody combination. Additionally, we also emphasized the molecular mechanism between 13H7 and SARS-CoV-2 NTD, revealing the impact of Y144 and H146 residue deletions and mutations on the neutralizing efficacy of 13H7. Taken together, our findings not only offer novel insights into the combination therapy of NTD and RBD neutralizing mAbs but also lay a theoretical foundation for the development of vaccines targeting NTD antibodies, thus providing valuable understanding of alleviating the emergence of SARS-CoV-2 variants.
History
DepositionJan 2, 2025-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62925.png

Downloads & links

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Map

FileDownload / File: emd_62925.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.7492249 - 1.3449693
Average (Standard dev.)-0.0002982659 (±0.014045892)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 448.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62925_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_62925_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 spike in complex with antibodies 9G11 and 3E2

EntireName: SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2
Components
  • Complex: SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2
    • Complex: The Fab of 3E2
      • Protein or peptide: Light chain of 3E2
      • Protein or peptide: Heavy chain of 3E2
    • Complex: SARS-CoV-2 spike
      • Protein or peptide: Spike protein S1
    • Complex: The Fab of 9G11
      • Protein or peptide: Light chain of 9G11
      • Protein or peptide: Heavy chain of 9G11
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2

SupramoleculeName: SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: The Fab of 3E2

SupramoleculeName: The Fab of 3E2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: SARS-CoV-2 spike

SupramoleculeName: SARS-CoV-2 spike / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #4: The Fab of 9G11

SupramoleculeName: The Fab of 9G11 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 25.122336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF ...String:
RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF NCYFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNF

UniProtKB: Spike glycoprotein

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Macromolecule #2: Light chain of 3E2

MacromoleculeName: Light chain of 3E2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.203357 KDa
SequenceString:
QIVLTQSPAI MSASLGEEIT LTCSVSSSVS DMHWYQQKSG TSPKVFIYST SNLASGVPSR FSGSGSGTFY SLTISSVEAE DAAYYYCHQ WSSWTFGGGT KLEIK

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Macromolecule #3: Heavy chain of 3E2

MacromoleculeName: Heavy chain of 3E2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.105676 KDa
SequenceString:
EVMLVESGGG VVKPGGSLKL SCAASGFSFS TYAMSWIRQT PEKSLEWVAA ISSGGTNTYY PGSVKGRFTI SRDKAMNTLY LQLSSLRSE DTAMYYCVRH SGNYVDSVMD YWGQGTSVTV SS

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Macromolecule #4: Light chain of 9G11

MacromoleculeName: Light chain of 9G11 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.809047 KDa
SequenceString:
DIVMTQSQKF MSTSVGDRVS VTCKASQNVG TNVAWYQQKP GQPPKALIYS ASYRYSGVPD RFTGSGSGTD FTLTISNVQS EDLAEYFCQ QYNSYPWTFG GGTKLEIK

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Macromolecule #5: Heavy chain of 9G11

MacromoleculeName: Heavy chain of 9G11 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.080461 KDa
SequenceString:
QVQLQQPGAE LVKPGASVKM SCKASGYTFT SYSMHWVKQT PGQGLEWIGA IYPGIGDTSY NQKFKGKATL TADKSSSTAY MQLSSLTSE DSAVYYCTRD GYPDYYALDY WGQGTSVTVS S

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.416 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 307127
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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