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- EMDB-39262: Cryo-EM structure of simian rotavirus SA11 VP4 in complex with nA... -

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Entry
Database: EMDB / ID: EMD-39262
TitleCryo-EM structure of simian rotavirus SA11 VP4 in complex with nAb 7H13 at Low concentration
Map data
Sample
  • Complex: Immune complex of rotavirus with low concentrated 7H13
    • Complex: Rotavirus VP4
    • Complex: Fab 7H13
KeywordsVIRUS / ROTAVIRUS / VP4
Biological speciesRotavirus A / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsHuang Y / Sun H / Zheng Q / Li S / Ge S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: A single residue switch mediates the broad neutralization of Rotaviruses.
Authors: Yang Huang / Feibo Song / Yuanjun Zeng / Hui Sun / Roufang Sheng / Xuechun Wang / Liqin Liu / Guoxing Luo / Yanan Jiang / Yaling Chen / Mengxuan Zhang / Shiyin Zhang / Ying Gu / Hai Yu / ...Authors: Yang Huang / Feibo Song / Yuanjun Zeng / Hui Sun / Roufang Sheng / Xuechun Wang / Liqin Liu / Guoxing Luo / Yanan Jiang / Yaling Chen / Mengxuan Zhang / Shiyin Zhang / Ying Gu / Hai Yu / Shaowei Li / Tingdong Li / Qingbing Zheng / Shengxiang Ge / Jun Zhang / Ningshao Xia /
Abstract: Broadly neutralizing antibodies (bNAbs) could offer escape-tolerant and lasting protection against viral infections and therefore guide development of broad-spectrum vaccines. The increasing ...Broadly neutralizing antibodies (bNAbs) could offer escape-tolerant and lasting protection against viral infections and therefore guide development of broad-spectrum vaccines. The increasing challenge posed by viral evolution and immune evasion intensifies the importance of the discovery of bNAbs and their underlying neutralization mechanism. Here, focusing on the pivotal viral protein VP4 of rotavirus (RV), we identify a potent bNAb, 7H13, exhibiting broad-spectrum neutralization across diverse RV genotypes and demonstrating strong prevention of virus infection in female mice. A combination of time-resolved cryo-electron microscopy (cryo-EM) and in situ cryo-electron tomography (cryo-ET) analysis reveals a counterintuitive dynamic process of virus inactivation, in which 7H13 asymmetrically binds to a conserved epitope in the capsid-proximal aspect of VP4, triggers a conformational switch in a critical residue-F418-thereby disrupts the meta-stable conformation of VP4 essential for normal viral infection. Structure-guided mutagenesis corroborates the essential role of the 7H13 heavy chain I54 in activating F418 switch and destabilizing VP4. These findings define an atypical NAbs' neutralization mechanism and reveal a potential type of virus vulnerable site for universal vaccine and therapeutics design.
History
DepositionFeb 26, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39262.png

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Map

FileDownload / File: emd_39262.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.001895836 - 2.3197093
Average (Standard dev.)0.0006999527 (±0.019965658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39262_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_39262_half_map_2.map
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Sample components

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Entire : Immune complex of rotavirus with low concentrated 7H13

EntireName: Immune complex of rotavirus with low concentrated 7H13
Components
  • Complex: Immune complex of rotavirus with low concentrated 7H13
    • Complex: Rotavirus VP4
    • Complex: Fab 7H13

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Supramolecule #1: Immune complex of rotavirus with low concentrated 7H13

SupramoleculeName: Immune complex of rotavirus with low concentrated 7H13
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Rotavirus A / Strain: SA11

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Supramolecule #2: Rotavirus VP4

SupramoleculeName: Rotavirus VP4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Rotavirus A / Strain: SA11

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Supramolecule #3: Fab 7H13

SupramoleculeName: Fab 7H13 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#7
Source (natural)Organism: Mus musculus (house mouse)

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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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 392037
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: cryosparc local refine
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: cryosparc local refine

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