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- EMDB-62589: Cryo-EM structure of SARS-CoV-2 prototype spike protein in comple... -

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Entry
Database: EMDB / ID: EMD-62589
TitleCryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11
Map data
Sample
  • Complex: SARS-CoV-2 protoype spike protein in complex with triple-nAb 3G5, 4C11 and 4H5
    • Complex: SARS-CoV-2 prototype spike protein
      • Protein or peptide: Spike protein S1
    • Complex: The fragments of triple-nAb 3G5,4C11 and 4H5
      • Protein or peptide: The heavy chain of 4C11
      • Protein or peptide: The light chain of 4C11
      • Protein or peptide: The heavy chain of 4H5
      • Protein or peptide: The light chain of 4H5
      • Protein or peptide: The heavy chain of 3G5
      • Protein or peptide: The light chain of 3G5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / 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 / Mus musculus (house mouse) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsSun H / Jiang Y / Wang S / Zheng Z / Li S / Zheng Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Broad neutralizing antibody response of a monomeric spike-based SARS-CoV-2 bivalent vaccine against diverse variants.
Authors: Siling Wang / Hui Sun / Yizhen Wang / Zikang Wang / Lunzhi Yuan / Huilin Guo / Jiahua Gao / Miaolin Lan / Yangtao Wu / Huixian Shang / Xiuting Chen / Zheng Chen / Jiayi Hu / Zimin Tang / ...Authors: Siling Wang / Hui Sun / Yizhen Wang / Zikang Wang / Lunzhi Yuan / Huilin Guo / Jiahua Gao / Miaolin Lan / Yangtao Wu / Huixian Shang / Xiuting Chen / Zheng Chen / Jiayi Hu / Zimin Tang / Guiping Wen / Dong Ying / Chang Liu / Yanan Jiang / Jinfu Su / Min Lin / Ting Wu / Shaowei Li / Tianying Zhang / Jun Zhang / Yi Guan / Ningshao Xia / Quan Yuan / Qingbing Zheng / Yali Zhang / Zizheng Zheng /
Abstract: severeacute respiratory syndrome coronavirus 2 (SARS-CoV-2) bivalent vaccines show potential against variants but lack a full understanding of the immunological mechanisms that drive broadly ...severeacute respiratory syndrome coronavirus 2 (SARS-CoV-2) bivalent vaccines show potential against variants but lack a full understanding of the immunological mechanisms that drive broadly neutralizing antibodies (bnAbs). This study explored the immunogenicity of a bivalent vaccine in rhesus macaques, containing spike (S) proteins from the prototype (S) and chimeric S protein (S). The vaccine induced bnAbs against multiple variants, including challenging subvariants like EG.1, BA.2.86, and JN.1. The monomeric S protein exposed less accessible regions within the receptor-binding domain (RBD) "inner face" and "NTD face" and subdomains 1, eliciting a diverse array of bnAbs against various Omicron subvariants. Notably, antibodies targeting the conserved RBD inner face, such as 4A5, showed potent neutralization across all tested variants. Structural analyses provide insights into the broad protectiveness of these vaccine-elicited nAbs. This study underscores the potential of bivalent vaccines with monomeric spike proteins to confer broad-spectrum immunity, offering a promising direction for future SARS-CoV-2 universal vaccine design.
History
DepositionDec 5, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62589.png

Downloads & links

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Map

FileDownload / File: emd_62589.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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0017932967 - 2.3695414
Average (Standard dev.)0.0008676485 (±0.02051732)
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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Half map: #2

Fileemd_62589_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62589_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 protoype spike protein in complex with triple-nAb 3G5,...

EntireName: SARS-CoV-2 protoype spike protein in complex with triple-nAb 3G5, 4C11 and 4H5
Components
  • Complex: SARS-CoV-2 protoype spike protein in complex with triple-nAb 3G5, 4C11 and 4H5
    • Complex: SARS-CoV-2 prototype spike protein
      • Protein or peptide: Spike protein S1
    • Complex: The fragments of triple-nAb 3G5,4C11 and 4H5
      • Protein or peptide: The heavy chain of 4C11
      • Protein or peptide: The light chain of 4C11
      • Protein or peptide: The heavy chain of 4H5
      • Protein or peptide: The light chain of 4H5
      • Protein or peptide: The heavy chain of 3G5
      • Protein or peptide: The light chain of 3G5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 protoype spike protein in complex with triple-nAb 3G5,...

SupramoleculeName: SARS-CoV-2 protoype spike protein in complex with triple-nAb 3G5, 4C11 and 4H5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: SARS-CoV-2 prototype spike protein

SupramoleculeName: SARS-CoV-2 prototype 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: The fragments of triple-nAb 3G5,4C11 and 4H5

SupramoleculeName: The fragments of triple-nAb 3G5,4C11 and 4H5 / 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: The heavy chain of 4C11

MacromoleculeName: The heavy chain of 4C11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.431928 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVESGGD LVKPGGSLRL SCVASGFTFS RHEMHWVRQA PGEGLEWLSV ISETGGTTYY ADSVKGRFTI SRDNAKNSVF LQMNSLRAE DTAVYFCVRD GGDPAGTVRF FDYWGQGVLV TVSS

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Macromolecule #2: The light chain of 4C11

MacromoleculeName: The light chain of 4C11 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.567954 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIQMSQSPSS LSASVGDRVT ITCRASQGIT SFLNWYQKKP GKAPTLLIYS SNRLASAVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QYISFPLTFG GGTKVELK

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Macromolecule #3: The heavy chain of 4H5

MacromoleculeName: The heavy chain of 4H5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.104521 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLQESGPG LVKPSETLSL TCAVSGGSIS SGYGWNWIRQ PPGKGLEWVG YIYGSSGSTN YNPSLKNRVT ISKDASKNQF SLKVRSVTA TDTAIYYCAR DTYPSAWSWG YWGQGVLVTV SS

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Macromolecule #4: The light chain of 4H5

MacromoleculeName: The light chain of 4H5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.750836 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSVLTQPPSV SGAPGQKVTI SCTGSSSNIE VYDVHWYQQL PGTAPKLLIY DNNQRPSGIS DRFSGSKSGT SASLAITGLQ TEDEADYYC QSYDTSLNAY IFGAGTRLTV L

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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
Molecular weightTheoretical: 21.772391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN ...String:
NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGP

UniProtKB: Spike glycoprotein

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Macromolecule #6: The heavy chain of 3G5

MacromoleculeName: The heavy chain of 3G5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 12.78621 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLQESGPG LVKPSETLSL TCAVSGVSIS SFLWNWIRQP PGKGLEWIGE INGNSGSTYY NPSLKSRVTI SKDASKSQFS LILGSVTAA DTAVYYCATR DSGPRGVDDY WGQGVLVTVS S

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Macromolecule #7: The light chain of 3G5

MacromoleculeName: The light chain of 3G5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 12.25778 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIVMTQIPLS LPVTPGEPAS ISCRSSQTLL HSGSAHTSLD WYLQKPGQSP QLLIYMVSNR ASGVPDRFSG SGSGTDFTLK ISRVEAEDV GVYYCMQSVD FPYSFGQGTK VEIK

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / 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: 1.8 µm / Nominal defocus min: 1.0 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: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63542
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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