[English] 日本語
Yorodumi
- EMDB-62323: Cryo-EM structure of simian rotavirus SA11 TLP in complex with nA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62323
TitleCryo-EM structure of simian rotavirus SA11 TLP in complex with nAb 41# (37 degree Celsius, 1 h)
Map data
Sample
  • Complex: Immune complex of rotavirus SA11 TLP with antibody 41# following a 1-hour incubation at 37 degree Celsius
    • Complex: Mature rotavirus triple-layered particle
    • Complex: Fab 41#
KeywordsVIRUS / ROTAVIRUS / IMMUNE COMPLEX
Biological speciesRotavirus A / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsHuang Y / Sun H / Song F / Zheng Q / Li 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
DepositionNov 9, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62323.png

Downloads & links

-
Map

FileDownload / File: emd_62323.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 640 pix.
= 1280. Å		2 Å/pix.
x 640 pix.
= 1280. Å		2 Å/pix.
x 640 pix.
= 1280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.37718704 - 0.70339876
Average (Standard dev.)-0.0021247522 (±0.055876125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 1280.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_62323_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62323_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Immune complex of rotavirus SA11 TLP with antibody 41# following ...

EntireName: Immune complex of rotavirus SA11 TLP with antibody 41# following a 1-hour incubation at 37 degree Celsius
Components
  • Complex: Immune complex of rotavirus SA11 TLP with antibody 41# following a 1-hour incubation at 37 degree Celsius
    • Complex: Mature rotavirus triple-layered particle
    • Complex: Fab 41#

-
Supramolecule #1: Immune complex of rotavirus SA11 TLP with antibody 41# following ...

SupramoleculeName: Immune complex of rotavirus SA11 TLP with antibody 41# following a 1-hour incubation at 37 degree Celsius
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rotavirus A / Strain: SA11

-
Supramolecule #2: Mature rotavirus triple-layered particle

SupramoleculeName: Mature rotavirus triple-layered particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rotavirus A / Strain: SA11

-
Supramolecule #3: Fab 41#

SupramoleculeName: Fab 41# / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9213
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: cryosparc Non-uniform Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: cryosparc Non-uniform Refinement

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more