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- EMDB-56837: E. coli 70S ribosome with P/E-site tRNA -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56837
TitleE. coli 70S ribosome with P/E-site tRNA
Map data70S main map
Sample
  • Complex: E. coli 70S ribosome
Keywords70S ribosome / RNA excited states / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.31 Å
AuthorsSteinmetzger C / Riad M / Petzold K
Funding supportEuropean Union, Sweden, 11 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 1011-2020European Union
H2020 Marie Curie Actions of the European Commission747446European Union
The Swedish Foundation for Strategic ResearchICA14-0023 Sweden
Swedish Research Council2014-04303 Sweden
Swedish Research Council2018-00250 Sweden
Ake Wiberg Foundation467080968European Union
Ake Wiberg FoundationM14-0109European Union
Other privateJS20140009 Sweden
Carl Trygger FoundationCTS14-383 Sweden
Carl Trygger FoundationCTS15-383 Sweden
Other privateM91/14 Sweden
CitationJournal: Biorxiv / Year: 2026
Title: Universal 3D Motif dynamics in RNA: The A-minor Switch
Authors: Steinmetzger C / Karlsson H / Fontana C / Galindo Riera N / Riad M / Kosek D / Schlagnitweit J / Steiner E / Friebe Sandoz S / Andersson ER / Petzold K
History
DepositionFeb 20, 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_56837.png

Downloads & links

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Map

FileDownload / File: emd_56837.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 576 pix.
= 436.896 Å		0.76 Å/pix.
x 576 pix.
= 436.896 Å		0.76 Å/pix.
x 576 pix.
= 436.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7585 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0695
Minimum - Maximum-0.25607887 - 0.7488937
Average (Standard dev.)0.0003459812 (±0.021243725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 436.896 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56837_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 70S map filtered to local resolution

Fileemd_56837_additional_1.map
Annotation70S map filtered to local resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 70S half map B

Fileemd_56837_half_map_1.map
Annotation70S half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 70S half map A

Fileemd_56837_half_map_2.map
Annotation70S half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli 70S ribosome

EntireName: E. coli 70S ribosome
Components
  • Complex: E. coli 70S ribosome

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Supramolecule #1: E. coli 70S ribosome

SupramoleculeName: E. coli 70S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#55
Source (natural)Organism: Escherichia coli (E. coli) / Strain: SQ171fg

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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: 7.6
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 34872
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.1)
FSC plot (resolution estimation)

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