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- EMDB-57777: Map of the 70S ribosome with E- and P-site tRNA from the alphapro... -

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Basic information

Entry
Database: EMDB / ID: EMD-57777
TitleMap of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.
Map dataMap of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.
Sample
  • Complex: Map of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.
KeywordsRibosome / 70S / E-site tRNA / P-site tRNA
Biological speciesRhodospirillum rubrum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 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_57777.png

Downloads & links

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Map

FileDownload / File: emd_57777.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 750 pix.
= 532.5 Å		0.71 Å/pix.
x 750 pix.
= 532.5 Å		0.71 Å/pix.
x 750 pix.
= 532.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0641
Minimum - Maximum-0.2543006 - 0.5521554
Average (Standard dev.)-0.00080516527 (±0.022284577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions750750750
Spacing750750750
CellA=B=C: 532.5 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_57777_half_map_1.map
AnnotationHalf map A for "Structure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum".
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_57777_half_map_2.map
AnnotationHalf map B for "Structure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum".
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 alphapro...

EntireName: Map of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.
Components
  • Complex: Map of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.

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

SupramoleculeName: Map of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rhodospirillum rubrum (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 GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.6 µm / Nominal defocus min: 0.2 µm

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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 reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.2)
Software - details: cryoSPARC was used to process cryo-EM data
Number images used: 23190
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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