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- EMDB-62733: Focused refinement up-RBD2 of SARS-CoV-2 EG.5.1 Variant Spike pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-62733
TitleFocused refinement up-RBD2 of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-203
Map data
Sample
  • Complex: EG.5.1 spike protein (S) in complex with antibody XGi-203
    • Complex: XGi-203 heavy chain
    • Complex: XGi-203 light chain
    • Complex: EG.5.1 Spike glycoprotein
KeywordsSpike-antibody complex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsQiu YN / Sun L
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
National Key Research and Development Program2021YFC2302500 China
R&D Program of Guangzhou LaboratorySRPG22-003 China
CitationJournal: Nat Commun / Year: 2025
Title: Orphan broadly RBD-binding antibodies annotate three remaining conserved RBD epitopes along SARS-CoV-2 evolution.
Authors: Minxiang Xie / Yinong Qiu / Xiaoyu Zhao / Jialu Shi / Yuanchen Liu / Qingsong Zhang / Jiaying He / Jiayan Li / Luotian Liu / Siyuan Sun / Yuzhen Zhu / Qiyu Mao / Yiming Long / Thiago Y ...Authors: Minxiang Xie / Yinong Qiu / Xiaoyu Zhao / Jialu Shi / Yuanchen Liu / Qingsong Zhang / Jiaying He / Jiayan Li / Luotian Liu / Siyuan Sun / Yuzhen Zhu / Qiyu Mao / Yiming Long / Thiago Y Oliveira / Zijun Wang / Yunjiao Zhou / Yan Yan / Anqi Xia / Wenjing Zai / Christian T Mayer / Youhua Xie / Shibo Jiang / Lu Lu / Rong Xia / Fan Wu / Lei Sun / Pengfei Wang / Hin Chu / Qiao Wang /
Abstract: The receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein continues to evolve, facilitating antibody evasion. It remains unclear whether any conserved RBD epitopes persist across SARS-CoV- ...The receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein continues to evolve, facilitating antibody evasion. It remains unclear whether any conserved RBD epitopes persist across SARS-CoV-2 variants and whether vaccination and/or breakthrough infection (BTI) can elicit antibodies capable of targeting these conserved regions to counter future variants. Here, using a heterogeneous double-bait single B-cell sorting strategy, we identify a subset of antibodies with broad-spectrum RBD binding, including recognition of SARS-CoV-1 and emerging variants such as EG.5.1, BA.2.86, JN.1, and KP.2/3. These broadly binding antibodies (bbAbs) exhibit elevated levels of somatic hypermutation but are infrequently derived from clonally expanded B lymphocytes. Passive transfer of representative bbAbs reduces viral infection in a male hamster model. Structural analyses reveals that these bbAbs primarily target three distinct, highly conserved RBD epitopes, suggesting potential regions of future mutational pressure and highlighting the presence of conserved and immunogenic RBD conformations that may serve as a foundation for the development of broadly protective vaccines.
History
DepositionDec 13, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62733.png

Downloads & links

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Map

FileDownload / File: emd_62733.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 298.24 Å		0.93 Å/pix.
x 320 pix.
= 298.24 Å		0.93 Å/pix.
x 320 pix.
= 298.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0017637549 - 1.7269293
Average (Standard dev.)0.000579263 (±0.015409445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 298.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62733_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62733_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 : EG.5.1 spike protein (S) in complex with antibody XGi-203

EntireName: EG.5.1 spike protein (S) in complex with antibody XGi-203
Components
  • Complex: EG.5.1 spike protein (S) in complex with antibody XGi-203
    • Complex: XGi-203 heavy chain
    • Complex: XGi-203 light chain
    • Complex: EG.5.1 Spike glycoprotein

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Supramolecule #1: EG.5.1 spike protein (S) in complex with antibody XGi-203

SupramoleculeName: EG.5.1 spike protein (S) in complex with antibody XGi-203
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: XGi-203 heavy chain

SupramoleculeName: XGi-203 heavy chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: XGi-203 light chain

SupramoleculeName: XGi-203 light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: EG.5.1 Spike glycoprotein

SupramoleculeName: EG.5.1 Spike glycoprotein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32232
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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