[English] 日本語
Yorodumi
- EMDB-2826: Structure of the membrane-bound mitoribosome from yeast -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2826
TitleStructure of the membrane-bound mitoribosome from yeast
Map dataSubtomogram average of the membrane-bound mitoribosome from yeast
Sample
  • Sample: Membrane-bound mitoribosome in isolated mitochondria from yeast
  • Complex: Membrane-bound 73S mitoribosome
Keywordsribosome / mitoribosome / mitochondria / Mba1 / tomography subtomogram analysis
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 30.0 Å
AuthorsPfeffer S / Woellhaf MW / Herrmann JM / Foerster F
CitationJournal: Nat Commun / Year: 2015
Title: Organization of the mitochondrial translation machinery studied in situ by cryoelectron tomography.
Authors: Stefan Pfeffer / Michael W Woellhaf / Johannes M Herrmann / Friedrich Förster /
Abstract: Whereas the structure and function of cytosolic ribosomes have been studied in great detail, we know surprisingly little about the structural basis of mitochondrial protein synthesis. Here we used ...Whereas the structure and function of cytosolic ribosomes have been studied in great detail, we know surprisingly little about the structural basis of mitochondrial protein synthesis. Here we used cryoelectron tomography and subtomogram analysis to visualize mitoribosomes in isolated yeast mitochondria, avoiding perturbations during ribosomal purification. Most mitoribosomes reside in immediate proximity to the inner mitochondrial membrane, in line with their specialization in the synthesis of hydrophobic membrane proteins. The subtomogram average of membrane-associated mitoribosomes reveals two distinct membrane contact sites, formed by the 21S rRNA expansion segment 96-ES1 and the inner membrane protein Mba1. On the basis of our data, we further hypothesize that Mba1 is not just a passive mitoribosome receptor on the inner membrane, but that it spatially aligns mitoribosomes with the membrane insertion machinery. This study reveals detailed insights into the supramolecular organization of the mitochondrial translation machinery and its association with the inner membrane in translation-competent mitochondria.
History
DepositionNov 24, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseJan 28, 2015-
UpdateJan 28, 2015-
Current statusJan 28, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2826.tif

Downloads & links

-
Map

FileDownload / File: emd_2826.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of the membrane-bound mitoribosome from yeast
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.62 Å/pix.
x 200 pix.
= 524. Å		2.62 Å/pix.
x 200 pix.
= 524. Å		2.62 Å/pix.
x 200 pix.
= 524. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-7.4176054 - 10.51815319
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 524.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z524.000524.000524.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-7.41810.5180.000

-
Supplemental data

-
Sample components

-
Entire : Membrane-bound mitoribosome in isolated mitochondria from yeast

EntireName: Membrane-bound mitoribosome in isolated mitochondria from yeast
Components
  • Sample: Membrane-bound mitoribosome in isolated mitochondria from yeast
  • Complex: Membrane-bound 73S mitoribosome

-
Supramolecule #1000: Membrane-bound mitoribosome in isolated mitochondria from yeast

SupramoleculeName: Membrane-bound mitoribosome in isolated mitochondria from yeast
type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Membrane-bound 73S mitoribosome

SupramoleculeName: Membrane-bound 73S mitoribosome / type: complex / ID: 1 / Name.synonym: 73S mitoribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: D273-10B / synonym: Budding yeast / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6 / Details: 20 mM Hepes pH 7.6, 50 mM KCl, 2 mM MgCl2
StainingType: NEGATIVE / Details: No staining
GridDetails: Lacey carbon molybdenum grids
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 60 % / Instrument: FEI VITROBOT MARK IV / Method: Blot time: 4s; blot force: 0

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DateNov 10, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsTomogram reconstruction and template matching against a single particle cryo-EM reconstruction of the 73S yeast mitoribosome were accomplished using PyTom. Tomogram areas corresponding to cross correlation peaks within mitochondria were visually inspected to identify true positive matches. For the retained coordinates, unbinned subtomograms were reconstructed individually from the weighted projections and iteratively aligned using PyTom. Aligned subtomograms were classified using constrained principal component analysis.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: PyTom, tom_toolbox, av3_toolbox / Number subtomograms used: 900
CTF correctionDetails: each micrograph

+
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