[English] 日本語
Yorodumi
- EMDB-1698: Three-dimensional structure of TspO by electron cryo-microscopy o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1698
TitleThree-dimensional structure of TspO by electron cryo-microscopy of helical crystals.
Map dataThe map contains 120 Angstrom thick slab through the tube reconstruction.
Sample
  • Sample: TspO and Escherichia coli polar lipid extract
  • Organelle or cellular component: Lipid extract
  • Protein or peptide: TspO
KeywordsTSPO / PBR / membrane protein / helical crystal
Biological speciesEscherichia coli (E. coli) / Rhodobacter sphaeroides (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 10.2 Å
AuthorsKorkhov VM / Sachse C / Short JM / Tate CG
CitationJournal: Structure / Year: 2010
Title: Three-dimensional structure of TspO by electron cryomicroscopy of helical crystals.
Authors: Vladimir M Korkhov / Carsten Sachse / Judith M Short / Christopher G Tate /
Abstract: The 18 kDa TSPO protein is a polytopic mitochondrial outer membrane protein involved in a wide range of physiological functions and pathologies, including neurodegeneration and cancer. The ...The 18 kDa TSPO protein is a polytopic mitochondrial outer membrane protein involved in a wide range of physiological functions and pathologies, including neurodegeneration and cancer. The pharmacology of TSPO has been extensively studied, but little is known about its biochemistry, oligomeric state, and structure. We have expressed, purified, and characterized a homologous protein, TspO from Rhodobacter sphaeroides, and reconstituted it as helical crystals. Using electron cryomicroscopy and single-particle helical reconstruction, we have determined a three-dimensional structure of TspO at 10 A resolution. The structure suggests that monomeric TspO comprises five transmembrane alpha helices that form a homodimer, which is consistent with the dimeric state observed in detergent solution. Furthermore, the arrangement of transmembrane domains of individual TspO subunits indicates a possibility of two substrate translocation pathways per dimer. The structure provides the first insight into the molecular architecture of TSPO/PBR protein family that will serve as a framework for future studies.
History
DepositionFeb 5, 2010-
Header (metadata) releaseJun 24, 2010-
Map releaseJun 24, 2010-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.75
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.75
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1698.tif

Downloads & links

-
Map

FileDownload / File: emd_1698.map.gz / Format: CCP4 / Size: 23.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map contains 120 Angstrom thick slab through the tube reconstruction.
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 1.75 / Movie #1: 1.75
Minimum - Maximum-2.11997 - 3.8827
Average (Standard dev.)0.0000000057552 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-125-125-50
Dimensions250250100
Spacing250250100
CellA: 300 Å / B: 300 Å / C: 120 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z250250100
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000120.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-125-125-50
NC/NR/NS250250100
D min/max/mean-2.1203.8830.000

-
Supplemental data

-
Sample components

-
Entire : TspO and Escherichia coli polar lipid extract

EntireName: TspO and Escherichia coli polar lipid extract
Components
  • Sample: TspO and Escherichia coli polar lipid extract
  • Organelle or cellular component: Lipid extract
  • Protein or peptide: TspO

-
Supramolecule #1000: TspO and Escherichia coli polar lipid extract

SupramoleculeName: TspO and Escherichia coli polar lipid extract / type: sample / ID: 1000 / Oligomeric state: Helical / Number unique components: 2
Molecular weightExperimental: 13.5 MDa / Theoretical: 13.5 MDa

-
Supramolecule #1: Lipid extract

SupramoleculeName: Lipid extract / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Lipid extract / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: TspO

MacromoleculeName: TspO / type: protein_or_peptide / ID: 1 / Name.synonym: TspO / Oligomeric state: Helical / Recombinant expression: Yes
Source (natural)Organism: Rhodobacter sphaeroides (bacteria) / synonym: Rhodobacter sphaeroides / Location in cell: Outer membrane
Molecular weightExperimental: 18 KDa / Theoretical: 18 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pUI2701

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris, 100 mM NaCl, 2 mM EDTA
VitrificationCryogen name: ETHANE / Chamber temperature: 77.2 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home built / Method: Back-side blotting
DetailsIncubated and dialysed for 3 days with Escherichia coli polar lipid extract

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.163 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateMay 30, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6 µm / Number real images: 36 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Segment-specific CTF
Final angle assignmentDetails: 2 degree increments, 0-360 degrees around helical axis, up to 12 degrees out-of-plane tilt
Final reconstructionApplied symmetry - Helical parameters - Δz: 32 Å
Applied symmetry - Helical parameters - Δ&Phi: 9.6 °
Applied symmetry - Helical parameters - Axial symmetry: D12 (2x12 fold dihedral)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: Imposition of 12-fold rotational symmetry
Details2 TspO molecules within dimer are related by an additional 2-fold axis parallel to tube axis.

+
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