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- EMDB-62590: Cryo-EM structure of SARS-CoV-2 prototype spike protein in comple... -

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Entry
Database: EMDB / ID: EMD-62590
TitleCryo-EM structure of SARS-CoV-2 prototype spike protein in complex with nAbs 4H1, 4A5, 4C1 and 2E10
Map data
Sample
  • Complex: SARS-CoV-2 prototype spike protein in complex with nAbs 4H1, 4A5, 4C1 and 2E10
    • Complex: SARS-CoV-2 spike protein
    • Complex: The fragments of four-nAb 4H1, 4A5, 4C1 and 2E10
KeywordsSARS-CoV-2 / Neutralizing antibody / Cryo-EM / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.41 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_62590.png

Downloads & links

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Map

FileDownload / File: emd_62590.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Slices (1/2)

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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-0.061611455 - 0.13559015
Average (Standard dev.)-0.00015895684 (±0.006192456)
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: #1

Fileemd_62590_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: #2

Fileemd_62590_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : SARS-CoV-2 prototype spike protein in complex with nAbs 4H1, 4A5,...

EntireName: SARS-CoV-2 prototype spike protein in complex with nAbs 4H1, 4A5, 4C1 and 2E10
Components
  • Complex: SARS-CoV-2 prototype spike protein in complex with nAbs 4H1, 4A5, 4C1 and 2E10
    • Complex: SARS-CoV-2 spike protein
    • Complex: The fragments of four-nAb 4H1, 4A5, 4C1 and 2E10

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Supramolecule #1: SARS-CoV-2 prototype spike protein in complex with nAbs 4H1, 4A5,...

SupramoleculeName: SARS-CoV-2 prototype spike protein in complex with nAbs 4H1, 4A5, 4C1 and 2E10
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: SARS-CoV-2 spike protein

SupramoleculeName: SARS-CoV-2 spike protein / 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 four-nAb 4H1, 4A5, 4C1 and 2E10

SupramoleculeName: The fragments of four-nAb 4H1, 4A5, 4C1 and 2E10 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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: 1.4000000000000001 µm / Nominal defocus min: 0.6 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: 7.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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