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- EMDB-32676: Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in... -

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Entry
Database: EMDB / ID: EMD-32676
TitleCryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies
    • Complex: neutralizing antibodies
      • Protein or peptide: 36H6 heavy chain
      • Protein or peptide: 83H7 light chain
      • Protein or peptide: 83H7 heavy chain
      • Protein or peptide: 85F7 heavy chain
      • Protein or peptide: 36H6 light chain
      • Protein or peptide: 85F7 light chain
    • Complex: spike protein STFK
      • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / spike / vaccine / neutralizing antibody / Cryo-EM / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN 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 region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / 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 speciesMus musculus (house mouse) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsZheng Q / Sun H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Host Microbe / Year: 2022
Title: Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine.
Authors: Yangtao Wu / Shaojuan Wang / Yali Zhang / Lunzhi Yuan / Qingbing Zheng / Min Wei / Yang Shi / Zikang Wang / Jian Ma / Kai Wang / Meifeng Nie / Jin Xiao / Zehong Huang / Peiwen Chen / Huilin ...Authors: Yangtao Wu / Shaojuan Wang / Yali Zhang / Lunzhi Yuan / Qingbing Zheng / Min Wei / Yang Shi / Zikang Wang / Jian Ma / Kai Wang / Meifeng Nie / Jin Xiao / Zehong Huang / Peiwen Chen / Huilin Guo / Miaolin Lan / Jingjing Xu / Wangheng Hou / Yunda Hong / Dabing Chen / Hui Sun / Hualong Xiong / Ming Zhou / Che Liu / Wenjie Guo / Huiyu Guo / Jiahua Gao / Congling Gan / Zhixiong Li / Haitao Zhang / Xinrui Wang / Shaowei Li / Tong Cheng / Qinjian Zhao / Yixin Chen / Ting Wu / Tianying Zhang / Jun Zhang / Hua Cao / Huachen Zhu / Quan Yuan / Yi Guan / Ningshao Xia /
Abstract: SARS-CoV-2 spread in humans results in continuous emergence of new variants, highlighting the need for vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation-patch ...SARS-CoV-2 spread in humans results in continuous emergence of new variants, highlighting the need for vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation-patch strategies, we engineered a recombinant monomeric spike variant (STFK1628x) that contains key regions and residues across multiple SAR-CoV-2 variants. STFK1628x demonstrated high immunogenicity and mutually complementary antigenicity to its prototypic form (STFK). In hamsters, a bivalent vaccine composed of STFK and STFK1628x elicited high titers of broad-spectrum neutralizing antibodies to 19 circulating SARS-CoV-2 variants, including Omicron sublineages BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, and BA.4/5. Furthermore, this vaccine conferred robust protection against intranasal challenges by either SARS-CoV-2 ancestral strain or immune-evasive Beta and Omicron BA.1. Strikingly, vaccination with the bivalent vaccine in hamsters effectively blocked within-cage virus transmission of ancestral SARS-CoV-2, Beta variant, and Omicron BA.1 to unvaccinated sentinels. Thus, our study provided insight and antigen candidates for the development of next-generation COVID-19 vaccines.
History
DepositionJan 23, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32676.png

Downloads & links

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Map

FileDownload / File: emd_32676.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 311.2 Å		0.78 Å/pix.
x 400 pix.
= 311.2 Å		0.78 Å/pix.
x 400 pix.
= 311.2 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: 0.08
Minimum - Maximum-0.42955515 - 0.5978903
Average (Standard dev.)-0.00012783842 (±0.010558087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 311.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in...

EntireName: Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies
    • Complex: neutralizing antibodies
      • Protein or peptide: 36H6 heavy chain
      • Protein or peptide: 83H7 light chain
      • Protein or peptide: 83H7 heavy chain
      • Protein or peptide: 85F7 heavy chain
      • Protein or peptide: 36H6 light chain
      • Protein or peptide: 85F7 light chain
    • Complex: spike protein STFK
      • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: neutralizing antibodies

SupramoleculeName: neutralizing antibodies / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5-#7
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: spike protein STFK

SupramoleculeName: spike protein STFK / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4

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Macromolecule #1: 36H6 heavy chain

MacromoleculeName: 36H6 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.129477 KDa
SequenceString:
VQLQQSGPEL VNPGASVKIS CKTSGYTFTE YTMHWVKQSH GKSLEWIGGI NPNNGDTIYN QKFKGKATLT VDKSSSTAYM ELRSLTSED SAVFYCAREG DYYVSSYGYW GQGTTLTVSS

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Macromolecule #2: 83H7 light chain

MacromoleculeName: 83H7 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.428608 KDa
SequenceString:
VMTQSHKFLS TSVGDRVNIT CKASQDVDTA VAWYQQKPGQ SPKLLISWAS TRHTGVPDRF TGSGSGTDFT LTISNVQSED LADYFCQQY SPYPYTFGGG TKLEI

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Macromolecule #3: 83H7 heavy chain

MacromoleculeName: 83H7 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.027506 KDa
SequenceString:
QLAQSGAELA RPGASVKLSC KASGYTFTRY WMQWVKQRPG QGLEWIGAIY PGDGDSRYTQ KFKGKATLTA DKSSSTAYMQ LSSLASEDS AVYYCARRNY YGYDAFAYWG QGTLVTVSA

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Macromolecule #4: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.344873 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA P

UniProtKB: Spike glycoprotein

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Macromolecule #5: 85F7 heavy chain

MacromoleculeName: 85F7 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.159612 KDa
SequenceString:
QVQLQQSGPE LVKPGASVRI SCKASGYTFT SYYIHWVKQR PGQGLEWIGW IYPGNVKSIY NEKFKGKATL TADKSSNTAY MQLSSLTSE DSAVYFCAGE EHGNYFDFWG QGTTLTVSQ

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Macromolecule #6: 36H6 light chain

MacromoleculeName: 36H6 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.440956 KDa
SequenceString:
DIVMSQSPSS LAVSVGEKVT MSCKSSQSLL YSSNQKNYLA WYQQKPGQSP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVKAEDL AVYYCQQYYS FPLTFGAGTK LELK

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Macromolecule #7: 85F7 light chain

MacromoleculeName: 85F7 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.278539 KDa
SequenceString:
QIVLSQSPTI LSASPGEKVT MTCRANSSVG FMHWCQQKPG SSPKPWIYAT SNLASGVPGR FSGSGSGTSY SLTISRVEAE DAATYYCQQ WSSDPPTFGS GTKLEIK

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / 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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 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: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162177
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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