[English] 日本語
Yorodumi
- EMDB-13287: polysome, ribosome pair (conformation 1) in Mycoplasma pneumoniae... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13287
Titlepolysome, ribosome pair (conformation 1) in Mycoplasma pneumoniae cells
Map data
Sample
  • Organelle or cellular component: cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
Biological speciesMycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsXue L / Lenz S / Rappsilber J / Mahamid J
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067 Germany
Citation
Journal: Nature / Year: 2022
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell.
Authors: Liang Xue / Swantje Lenz / Maria Zimmermann-Kogadeeva / Dimitry Tegunov / Patrick Cramer / Peer Bork / Juri Rappsilber / Julia Mahamid /
Abstract: Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to ...Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.
#1: Journal: Biorxiv / Year: 2021
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Authors: Xue L / Lenz S / Zimmermann-Kogadeeva M / Tegunov D / Cramer P / Bork P / Rappsilber J / Mahamid J
History
DepositionJul 30, 2021-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateOct 19, 2022-
Current statusOct 19, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13287.png

Downloads & links

-
Map

FileDownload / File: emd_13287.map.gz / Format: CCP4 / Size: 64 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 Å/pix.
x 256 pix.
= 768. Å		3 Å/pix.
x 256 pix.
= 768. Å		3 Å/pix.
x 256 pix.
= 768. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.67
Minimum - Maximum-0.6152958 - 2.2549913
Average (Standard dev.)0.017966144 (±0.13505171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 768.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_13287_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13287_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13287_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : cryo-electron tomograms of untreated Mycoplasma pneumoniae cells

EntireName: cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
Components
  • Organelle or cellular component: cryo-electron tomograms of untreated Mycoplasma pneumoniae cells

-
Supramolecule #1: cryo-electron tomograms of untreated Mycoplasma pneumoniae cells

SupramoleculeName: cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#55
Details: The tomograms were collected with intact Mycoplasma pneumoniae cells. The sub-tomograms extracted in silico from cellular tomograms are with large box size to accommodate two adjacent ...Details: The tomograms were collected with intact Mycoplasma pneumoniae cells. The sub-tomograms extracted in silico from cellular tomograms are with large box size to accommodate two adjacent ribosomes (one ribosome pair) with polysomes.
Source (natural)Organism: Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
Details: back-side blotting for 2-3 second before plunging using a manual plunger without an environmental chamber.
DetailsMycoplasma pneumoniae M129 cells grown on gold Quantifoil grids at 37 degrees Celsius before plunge freezing.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.2 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: 3.75 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 1154
ExtractionNumber tomograms: 356 / Number images used: 77539
Details: Initially 77539 sub-tomograms were extracted from 356 cells, with box size large enough to accommodate a di-ribosome. Then the polysome class with 9616 sub-tomograms were re-centered and re-extracted.
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more