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- EMDB-67083: Subtomogram average of in situ 70S ribosome using CRYO ARM 300II -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67083
TitleSubtomogram average of in situ 70S ribosome using CRYO ARM 300II
Map data
Sample
  • Complex: in Situ Ribosome from Salmonella enterica serovar Typhimurium
KeywordsRibosome
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 8.5 Å
AuthorsYanagisawa H / Miyata T / Kinoshita M / Kikkawa M / Namba K / Makino F
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22am121003 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
CitationJournal: AIMS Biophys / Year: 2026
Title: Subtomogram averaging by cryo electron tomography using CRYO ARMTM 300 II for purified and cellular samples
Authors: Makino F / Yanagisawa H / Eisenstein F / Miyata T / Kinoshita M / Kikkawa M / Namba K
History
DepositionNov 14, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67083.png

Downloads & links

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Map

FileDownload / File: emd_67083.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 140 pix.
= 476. Å		3.4 Å/pix.
x 140 pix.
= 476. Å		3.4 Å/pix.
x 140 pix.
= 476. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.14208297 - 0.3723393
Average (Standard dev.)0.000000000000698 (±0.030602684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 476.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67083_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67083_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_67083_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 : in Situ Ribosome from Salmonella enterica serovar Typhimurium

EntireName: in Situ Ribosome from Salmonella enterica serovar Typhimurium
Components
  • Complex: in Situ Ribosome from Salmonella enterica serovar Typhimurium

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Supramolecule #1: in Situ Ribosome from Salmonella enterica serovar Typhimurium

SupramoleculeName: in Situ Ribosome from Salmonella enterica serovar Typhimurium
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 5 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 30000

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, Warp) / Number subtomograms used: 16677
ExtractionNumber tomograms: 19 / Number images used: 41004 / Software - Name: RELION (ver. 5)
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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