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- EMDB-65044: Structure of SARS-CoV-2 Spike in complex with antibodies S309 and... -

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Entry
Database: EMDB / ID: EMD-65044
TitleStructure of SARS-CoV-2 Spike in complex with antibodies S309 and CT1-5.
Map data
Sample
  • Complex: Structure of SARS-CoV-2 Spike in complex with antibodies S309 and CT1-5.
KeywordsSARS-CoV-2 / Spike / Fab / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsJiang Y / Sun H / Zheng Q / Li S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2026
Title: Public antibody clonotypes and deep learning identify SARS-CoV-2 and HIV broadly neutralizing antibodies in immune repertoires.
Authors: Lizhi Zhou / Zhili Yu / Shutian Lin / Yanan Jiang / Jiahua Gao / Yue Ma / Wenling Jiang / Siting Liang / Yiqing Chen / Yiwen Zhang / Yanqing Lin / Min Liang / Jingyu Dai / Lisha Zhang / ...Authors: Lizhi Zhou / Zhili Yu / Shutian Lin / Yanan Jiang / Jiahua Gao / Yue Ma / Wenling Jiang / Siting Liang / Yiqing Chen / Yiwen Zhang / Yanqing Lin / Min Liang / Jingyu Dai / Lisha Zhang / Yuxuan Xiao / Tingting Li / Zhibo Kong / Qingyuan Liu / Shaogui He / Yangtao Wu / Quan Yuan / Fan Liu / Jun Zhang / Qingbing Zheng / Hai Yu / Ying Gu / Shaowei Li / Ningshao Xia /
Abstract: Broadly neutralizing antibodies (bnAbs) are essential for the development of vaccines and therapeutics against rapidly evolving pathogens like HIV and SARS-CoV-2, yet traditional discovery methods ...Broadly neutralizing antibodies (bnAbs) are essential for the development of vaccines and therapeutics against rapidly evolving pathogens like HIV and SARS-CoV-2, yet traditional discovery methods remain technically challenging and time consuming. Here, we introduce ClonoDeep, an AI-powered platform that integrates public antibody clonotypes with a sequence-based deep learning model to directly identify bnAbs from a large-scale immune repertoire, independent of antigen-specific immunization. Applied to SARS-CoV-2 repertoires, ClonoDeep identified 18 clonotype-derived antibody candidates; 83% of the candidates were neutralizing antibodies, and 8 of these antibodies demonstrated broad neutralization across variants. Structural analysis revealed that somatic hypermutations at HCDR3 His107/Gly109 are key enhancers of the binding affinity and neutralizing breadth. Extending to HIV, ClonoDeep uncovered three previously unreported bnAbs from non-HIV cohorts, indicating that rare bnAb-like precursors exist in non-HIV cohort repertoires. ClonoDeep establishes a high-throughput computational approach for mining neutralizing antibodies from antibody repertoires shaped by non-pathogen-specific immunity and provides design principles to guide vaccine strategies against genetically diverse pathogens.
History
DepositionJun 12, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65044.png

Downloads & links

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Map

FileDownload / File: emd_65044.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 720 pix.
= 468. Å		0.65 Å/pix.
x 720 pix.
= 468. Å		0.65 Å/pix.
x 720 pix.
= 468. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.2149767 - 0.4202252
Average (Standard dev.)-0.00039940723 (±0.008305808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 467.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65044_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_65044_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of SARS-CoV-2 Spike in complex with antibodies S309 and...

EntireName: Structure of SARS-CoV-2 Spike in complex with antibodies S309 and CT1-5.
Components
  • Complex: Structure of SARS-CoV-2 Spike in complex with antibodies S309 and CT1-5.

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Supramolecule #1: Structure of SARS-CoV-2 Spike in complex with antibodies S309 and...

SupramoleculeName: Structure of SARS-CoV-2 Spike in complex with antibodies S309 and CT1-5.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.4 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: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49476
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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