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- EMDB-57779: Map of the 70S ribosome with E- and P-site tRNA from the gammapro... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-57779
TitleMap of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.
Map dataStructure of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.
Sample
  • Complex: Map of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.
KeywordsRibosome / 70S / P-site tRNA / E-site tRNA
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChan LI / Omae K / Amikura K / Suzuki S / Melnikov SM
Funding support United Kingdom, Japan, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008695/1 United Kingdom
Royal SocietyICA/R2/242249 United Kingdom
Japan Science and TechnologyJPMJCR20S4 Japan
CitationJournal: To Be Published
Title: Hibernation factors are prone to structural divergence and spontaneous loss in bacterial species
Authors: Chan LI / Melnikov SV
History
DepositionApr 27, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57779.png

Downloads & links

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Map

FileDownload / File: emd_57779.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 500 pix.
= 605.455 Å		1.21 Å/pix.
x 500 pix.
= 605.455 Å		1.21 Å/pix.
x 500 pix.
= 605.455 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.8696789 - 1.8401695
Average (Standard dev.)-0.00014148366 (±0.05865931)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 605.45496 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A for "Structure of the 70S...

Fileemd_57779_half_map_1.map
AnnotationHalf map A for "Structure of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli".
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B for "Structure of the 70S...

Fileemd_57779_half_map_2.map
AnnotationHalf map B for "Structure of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli".
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Map of the 70S ribosome with E- and P-site tRNA from the gammapro...

EntireName: Map of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.
Components
  • Complex: Map of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.

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Supramolecule #1: Map of the 70S ribosome with E- and P-site tRNA from the gammapro...

SupramoleculeName: Map of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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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 III (4k x 4k) / Average electron dose: 50.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.2)
Software - details: cryoSPARC was used to process cryo-EM data
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.2) / Number images used: 147751
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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