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- EMDB-62592: Cryo-EM structure of SARS-CoV-2 EG.1 spike protein in complex wit... -

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Entry
Database: EMDB / ID: EMD-62592
TitleCryo-EM structure of SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10
Map data
Sample
  • Complex: SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10
    • Complex: SARS-CoV-2 spike protein of EG.1 variant
      • Protein or peptide: Spike protein S1
    • Complex: The fragments of triple-nAb 4A5, 4C1 and 2E10
      • Protein or peptide: 2E10 light chain
      • Protein or peptide: 4C1 heavy chain
      • Protein or peptide: 4C1 light chain
      • Protein or peptide: 2E10 heavy chain
      • Protein or peptide: 4A5 heavy chain
      • Protein or peptide: 4A5 light chain
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 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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_62592.png

Downloads & links

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Map

FileDownload / File: emd_62592.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.)
0.65 Å/pix.
x 400 pix.
= 260. Å		0.65 Å/pix.
x 400 pix.
= 260. Å		0.65 Å/pix.
x 400 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.032465167 - 1.9669728
Average (Standard dev.)0.0011035373 (±0.019852359)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local refinement on the interface of 2E10 and SD1

Fileemd_62592_additional_1.map
AnnotationLocal refinement on the interface of 2E10 and SD1
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_62592_half_map_1.map
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Half map: #1

Fileemd_62592_half_map_2.map
Projections & Slices
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Sample components

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Entire : SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1...

EntireName: SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10
Components
  • Complex: SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10
    • Complex: SARS-CoV-2 spike protein of EG.1 variant
      • Protein or peptide: Spike protein S1
    • Complex: The fragments of triple-nAb 4A5, 4C1 and 2E10
      • Protein or peptide: 2E10 light chain
      • Protein or peptide: 4C1 heavy chain
      • Protein or peptide: 4C1 light chain
      • Protein or peptide: 2E10 heavy chain
      • Protein or peptide: 4A5 heavy chain
      • Protein or peptide: 4A5 light chain

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Supramolecule #1: SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1...

SupramoleculeName: SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: SARS-CoV-2 spike protein of EG.1 variant

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

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Supramolecule #3: The fragments of triple-nAb 4A5, 4C1 and 2E10

SupramoleculeName: The fragments of triple-nAb 4A5, 4C1 and 2E10 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #3-#7
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: 2E10 light chain

MacromoleculeName: 2E10 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.792564 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVVFTQSHSV SGSPGQTVTI SCTRNSGSID SEYVQWYQQR PGSAPTTVIY RDNQRPSGVP DRFSGSIDSS SNSASLAISG LKSEDEADY YCQSADGNYN PFFGGGTRLT V

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: EG.5.1
Molecular weightTheoretical: 31.750863 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NFRVQPTESI VRFPNITNLC PFHEVFNATT FASVYAWNRK RISNCVADYS VIYNFAPFFA FKCYGVSPTK LNDLCFTNVY ADSFVIRGN EVSQIAPGQT GNIADYNYKL PDDFTGCVIA WNSNKLDSKP SGNYNYLYRL FRKSKLKPFE RDISTEIYQA G NKPCNGVA ...String:
NFRVQPTESI VRFPNITNLC PFHEVFNATT FASVYAWNRK RISNCVADYS VIYNFAPFFA FKCYGVSPTK LNDLCFTNVY ADSFVIRGN EVSQIAPGQT GNIADYNYKL PDDFTGCVIA WNSNKLDSKP SGNYNYLYRL FRKSKLKPFE RDISTEIYQA G NKPCNGVA GPNCYSPLQS YGFRPTYGVG HQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SN KKFLPFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITP

UniProtKB: Spike glycoprotein

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Macromolecule #3: 4C1 heavy chain

MacromoleculeName: 4C1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.201554 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVESGGG LAKPGGSLRL SCAASGFTFS SYWMNWVRQA PGKGLEWVSV INSGGDNAYY ADSVKGRFTT SRDNSKSTLS LQMNSLREE DTAVYYCAKD RNLYYYDSGY YTEFSFDYWG QGVLVTVSS

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Macromolecule #4: 4C1 light chain

MacromoleculeName: 4C1 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.531521 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSVLTQPPSV SGDPGQSVTI SCTGSSSNIG GYYVNWYQQF PGTAPKLLIY DDNNRPSGVS DRFSGSKSGT SASLTITGLQ PGDEADYHC SGWDSSLSAV LFGRGTRLTV L

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Macromolecule #5: 2E10 heavy chain

MacromoleculeName: 2E10 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.308933 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLMESGGG VVQPGGSLRL SCAASGFTFG DYALHWVRQA PGKGLEWVSG ITWTGTRTYY AGSVKGRFTI SRDNAKNSLY LQMTRLRAE DTAFYYCTKD RVAVGRPPSF DSWGQGVLVT VSS

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Macromolecule #6: 4A5 heavy chain

MacromoleculeName: 4A5 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.542273 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVESGGG LVKPGGSLRL SCVASGFTFS DYEMHWVRQA PGKGLEWVSV ISESGGTTYY ADSVKGRFTI SRDNAKNSLF LQMNSLRAE DTAVYYCTRV VIVVFTAMRH FDYWGQGVLV TVSS

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Macromolecule #7: 4A5 light chain

MacromoleculeName: 4A5 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.665923 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIQMTQSPSS LSAPVGDTVT ITCRASQGIN SYLNWFQQKP GKAPKLLIYD ASTLESGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCL QYNNYPFTFG PGTRLDIK

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 113049
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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