[English] 日本語
Yorodumi
- EMDB-2203: Characterization of the insertase for beta-barrel proteins of the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2203
TitleCharacterization of the insertase for beta-barrel proteins of the outer mitochondrial membrane. 3-D reconstruction of the TOB complex
Map data3D reconstruction of Tob55 dimers isolated using the 9xHis tag on the Tob55 subunit. The Tob55 dimer is a complex identified in all outer membrane preparations but isolated only when the his-tag is on tob55. The dimer co-purifies with the TOB complex and was identified as a subclass of particles present in the his-Tob55 data sets. The mol. wgt. is 101 kDa. Two-fold symmetry has been applied
Sample
  • Sample: Tob55 dimer
  • Protein or peptide: Tob55 short
KeywordsTOB/SAM complex / beta-barrel proteins / Tob55/Sam50 / mitochondria outer membrane
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.4 Å
AuthorsKlein A / Israel L / Lackey SWK / Nargang FE / Imhof A / Baumeister W / Neupert W / Thomas DR
CitationJournal: J Cell Biol / Year: 2012
Title: Characterization of the insertase for β-barrel proteins of the outer mitochondrial membrane.
Authors: Astrid Klein / Lars Israel / Sebastian W K Lackey / Frank E Nargang / Axel Imhof / Wolfgang Baumeister / Walter Neupert / Dennis R Thomas /
Abstract: The TOB-SAM complex is an essential component of the mitochondrial outer membrane that mediates the insertion of β-barrel precursor proteins into the membrane. We report here its isolation and ...The TOB-SAM complex is an essential component of the mitochondrial outer membrane that mediates the insertion of β-barrel precursor proteins into the membrane. We report here its isolation and determine its size, composition, and structural organization. The complex from Neurospora crassa was composed of Tob55-Sam50, Tob38-Sam35, and Tob37-Sam37 in a stoichiometry of 1:1:1 and had a molecular mass of 140 kD. A very minor fraction of the purified complex was associated with one Mdm10 protein. Using molecular homology modeling for Tob55 and cryoelectron microscopy reconstructions of the TOB complex, we present a model of the TOB-SAM complex that integrates biochemical and structural data. We discuss our results and the structural model in the context of a possible mechanism of the TOB insertase.
History
DepositionSep 12, 2012-
Header (metadata) releaseOct 10, 2012-
Map releaseNov 14, 2012-
UpdateJul 17, 2013-
Current statusJul 17, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2203.jpg

Downloads & links

-
Map

FileDownload / File: emd_2203.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of Tob55 dimers isolated using the 9xHis tag on the Tob55 subunit. The Tob55 dimer is a complex identified in all outer membrane preparations but isolated only when the his-tag is on tob55. The dimer co-purifies with the TOB complex and was identified as a subclass of particles present in the his-Tob55 data sets. The mol. wgt. is 101 kDa. Two-fold symmetry has been applied
Voxel sizeX=Y=Z: 1.78 Å
Density
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.14503084 - 1.68543327
Average (Standard dev.)0.00043378 (±0.05871786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 249.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z249.200249.200249.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.1451.6850.000

-
Supplemental data

-
Sample components

-
Entire : Tob55 dimer

EntireName: Tob55 dimer
Components
  • Sample: Tob55 dimer
  • Protein or peptide: Tob55 short

-
Supramolecule #1000: Tob55 dimer

SupramoleculeName: Tob55 dimer / type: sample / ID: 1000
Details: The complexes were monodisperse. A mitochondrial outer membrane complex which can be identified as a component of the outer mitochondrial membrane but whose function is unknown.
Oligomeric state: dimeric / Number unique components: 1
Molecular weightExperimental: 101 KDa / Theoretical: 101 KDa
Method: Blue native gel electrophoresis and Isotope dilution mass spectroscopy analysis of bands isolated from BNGE gels.

-
Macromolecule #1: Tob55 short

MacromoleculeName: Tob55 short / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: No
Source (natural)Organism: Neurospora crassa (fungus) / Strain: Tob55 short HT / Organelle: mitochondria / Location in cell: outer membrane
Molecular weightExperimental: 50.7 KDa / Theoretical: 50.7 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8.5
Details: 1mM PMSF, 0.08%(v/v) Triton X-100, 50 mM HEPES pH 8.5
GridDetails: lacey carbon films on 200 mesh Molybdenum grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Method: blot for 4-5 seconds before plunging with whatman filter paper #1

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 84270 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -3.7 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Gatan 656 side entry holder / Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected using the live FFT at imaging magnification.
DateOct 7, 2009
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20 e/Å2
Details: Images collected using TOM_acquisition software. 24800 dimers were identified in various his-Tob55 datasets. In the end 19500 were included in the final reconstruction. Two-fold symmetry was ...Details: Images collected using TOM_acquisition software. 24800 dimers were identified in various his-Tob55 datasets. In the end 19500 were included in the final reconstruction. Two-fold symmetry was applied during the last 5 rounds of refinement.
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Phase and astigmatism correction applied to each micrograph
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, TOM_toolbox
Details: Final maps were reconstructed from images that had stable alignment parameters over the last 4 rounds of refinement. Stable was defined by absolute accumulated changes in theta and psi of ...Details: Final maps were reconstructed from images that had stable alignment parameters over the last 4 rounds of refinement. Stable was defined by absolute accumulated changes in theta and psi of the projection matched of less than 10 degrees. 24800 dimers were identified in various his-Tob55 datasets. In the end 19500 were included in the final reconstruction. Two-fold symmetry was applied during the last 5 rounds of refinement.
Number images used: 1

+
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