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- EMDB-61640: Rotated2 states without factor from rattus norvegicus 80S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-61640
TitleRotated2 states without factor from rattus norvegicus 80S ribosome
Map data
Sample
  • Cell: hippocamal primary neuron of Rattus norvegicus
Keywords80S ribosome / RIBOSOME
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 8.1 Å
AuthorsJung M / Roh S
Funding support Korea, Republic Of, 5 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1C1C1004598 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A5A1018081 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4021220 Korea, Republic Of
National Research Foundation (NRF, Korea)2019M3E5D6063871 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A6C101A183 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Correlative voltage imaging and cryo-electron tomography bridge neuronal activity and molecular structure.
Authors: Mingyu Jung / Gwanho Ko / Dongsung Lim / Seonghoon Kim / Sojeong Kim / Young-Joon Kim / Myunghwan Choi / Soung-Hun Roh /
Abstract: Neurons exhibit varying electrophysiological properties due to dynamic changes in spatiotemporal molecular networks. In situ cryo-electron tomography (cryo-ET) provides advantages for high-resolution ...Neurons exhibit varying electrophysiological properties due to dynamic changes in spatiotemporal molecular networks. In situ cryo-electron tomography (cryo-ET) provides advantages for high-resolution visualization of macromolecular complexes within their cellular context. Although correlation with fluorescent labeling allows cryo-ET to target specific cellular regions, it does not adequately reflect the electrophysiological properties of heterogeneous neurons. To bridge high-resolution molecular imaging with electrophysiological properties of individual neurons, we develop a Correlative Voltage Imaging and cryo-ET (CoVET) technique. The nondestructive nature of voltage imaging is compatible with cryo-ET, enabling a direct correlation between neuronal electrophysiology and molecular structures. Neurons are clustered based on their electrophysiological properties, allowing for single-cell-guided structural analysis using cryo-ET. We analyze the translational landscapes of individual neurons and find distinct structural characteristics and spatial networks among ribosomes from different electrophysiological clusters. Our results highlight the importance of the correlation between the electrophysiological properties and molecular structures.
History
DepositionSep 24, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61640.png

Downloads & links

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Map

FileDownload / File: emd_61640.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.42 Å/pix.
x 200 pix.
= 484. Å		2.42 Å/pix.
x 200 pix.
= 484. Å		2.42 Å/pix.
x 200 pix.
= 484. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.84
Minimum - Maximum-1.0190363 - 3.9110122
Average (Standard dev.)0.100547254 (±0.39348575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 484.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61640_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_61640_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_61640_half_map_2.map
Projections & Slices
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Sample components

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Entire : hippocamal primary neuron of Rattus norvegicus

EntireName: hippocamal primary neuron of Rattus norvegicus
Components
  • Cell: hippocamal primary neuron of Rattus norvegicus

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Supramolecule #1: hippocamal primary neuron of Rattus norvegicus

SupramoleculeName: hippocamal primary neuron of Rattus norvegicus / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
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: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFalcon4i
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 7520
ExtractionNumber tomograms: 281 / Number images used: 446231
CTF correctionType: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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