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- EMDB-62599: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-62599
TitleCryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with three-nAb 8H12, 3E2 and 1C4
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with double nAbs 3E2 and 1C4
    • Complex: SARS-CoV-2 BA.1 spike protein
      • Protein or peptide: Spike protein S1
    • Complex: nAbs 8H12 and 3E2
      • Protein or peptide: Light chain of 3E2
      • Protein or peptide: Heavy chain of 3E2
      • Protein or peptide: Light chain of 8H12
      • Protein or peptide: Heavy chain of 8H12
      • Protein or peptide: Light chain of 1C4
      • Protein or peptide: Heavy chain of 1C4
KeywordsSARS-CoV-2 / Neutralizing antibody / Cryo-EM / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsSun H / Jiang Y / Li S / Zheng Q / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with three-nAb 8H12, 3E2 and 1C4
Authors: Sun H / Jiang Y / Li S / Zheng Q
History
DepositionDec 5, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62599.png

Downloads & links

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Map

FileDownload / File: emd_62599.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: 0.09
Minimum - Maximum-0.56984925 - 0.8310089
Average (Standard dev.)-0.00034070123 (±0.0099078845)
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: #1

Fileemd_62599_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_62599_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 : Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex wit...

EntireName: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with double nAbs 3E2 and 1C4
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with double nAbs 3E2 and 1C4
    • Complex: SARS-CoV-2 BA.1 spike protein
      • Protein or peptide: Spike protein S1
    • Complex: nAbs 8H12 and 3E2
      • Protein or peptide: Light chain of 3E2
      • Protein or peptide: Heavy chain of 3E2
      • Protein or peptide: Light chain of 8H12
      • Protein or peptide: Heavy chain of 8H12
      • Protein or peptide: Light chain of 1C4
      • Protein or peptide: Heavy chain of 1C4

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex wit...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with double nAbs 3E2 and 1C4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: SARS-CoV-2 BA.1 spike protein

SupramoleculeName: SARS-CoV-2 BA.1 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: nAbs 8H12 and 3E2

SupramoleculeName: nAbs 8H12 and 3E2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4, #6-#7
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Light chain of 3E2

MacromoleculeName: Light chain of 3E2 / type: protein_or_peptide / ID: 1 / 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 #2: Heavy chain of 3E2

MacromoleculeName: Heavy chain of 3E2 / type: protein_or_peptide / ID: 2 / 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 #3: Light chain of 8H12

MacromoleculeName: Light chain of 8H12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.945558 KDa
SequenceString:
DIVMTQFQKF MSTSVGDRVS ITCKASQNVR TAVAWYQQKP GQSPKAMIYL ASNRHRGVPD RFTGSGCGTD FTLTISNVQC EDLADYFCL QHRNYPLTFG GGTKLEIK

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Macromolecule #4: Heavy chain of 8H12

MacromoleculeName: Heavy chain of 8H12 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.240784 KDa
SequenceString:
EVKLEESGGG LVQPGGSMKL SCAASGFTFS DAWMDWVRQS PEKGLEWVAQ IRRKANNHAT YYAESVKGRF TISRDDSKSS VYLQMNSLR AEDTGIYYCI RGMTYAMDFW GQGTSVTVSS

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Macromolecule #5: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: BA.1, Omicron
Molecular weightTheoretical: 22.06992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TNLCPFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNLA PFFTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGNIADY NYKLPDDFTG CVIAWNSNKL DSKVSGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP L RSYSFRPT ...String:
TNLCPFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNLA PFFTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGNIADY NYKLPDDFTG CVIAWNSNKL DSKVSGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP L RSYSFRPT YGVGHQPYRV VVLSFELLHA PATVCG

UniProtKB: Spike glycoprotein

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Macromolecule #6: Light chain of 1C4

MacromoleculeName: Light chain of 1C4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.642854 KDa
SequenceString:
DIVLTQSPAT LSVTPGDNVS LSCRASQIIS NNLHWYQQKS HESPRLLIKY ASQSISGIPS RFSGSGSGTD FTLSINSVET EDFGMYFCQ QSNTWPLTCG SGTKLELN

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Macromolecule #7: Heavy chain of 1C4

MacromoleculeName: Heavy chain of 1C4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.3849 KDa
SequenceString:
QIQLVQSGPE LKKPGETVKI SCKASGYTFT DYGLNWVKQA PGKGLKWMGW INTYSGEPTY NDEFRGRFAF SLETSTITAY LKINNLKNE DTATYFCARG GNWDWYFDVW GAGTTVTVSS

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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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 286938
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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