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- EMDB-65321: Focused map for cryoEM structure of tobacco mosaic virus tRNA-lik... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65321
TitleFocused map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S (focused on tRNA-like structure)
Map data
Sample
  • Complex: tobacco 80S ribosome with tRNA-like structure
KeywordstRNA-like structure / ribosome / tobacco / Nicotiana benthamiana / tobacco mosaic virus / RNA structure / translation
Biological speciesNicotiana benthamiana (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLu G / Lin J
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130063 China
National Natural Science Foundation of China (NSFC)32471349 China
CitationJournal: To be published
Title: To be published
Authors: Lu G / Lin J
History
DepositionJul 10, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65321.png

Downloads & links

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Map

FileDownload / File: emd_65321.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 560 pix.
= 537.04 Å		0.96 Å/pix.
x 560 pix.
= 537.04 Å		0.96 Å/pix.
x 560 pix.
= 537.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.959 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.36574462 - 1.1460218
Average (Standard dev.)-0.0028184874 (±0.010223477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 537.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65321_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65321_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_65321_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : tobacco 80S ribosome with tRNA-like structure

EntireName: tobacco 80S ribosome with tRNA-like structure
Components
  • Complex: tobacco 80S ribosome with tRNA-like structure

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Supramolecule #1: tobacco 80S ribosome with tRNA-like structure

SupramoleculeName: tobacco 80S ribosome with tRNA-like structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#82
Source (natural)Organism: Nicotiana benthamiana (plant)

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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: FEI FALCON I (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 422599
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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