|Entry||Database: EMDB / ID: 1698|
|Title||Three-dimensional structure of TspO by electron cryo-microscopy of helical crystals.|
|Keywords||TSPO / PBR / membrane protein / helical crystal|
|Sample||TspO and Escherichia coli polar lipid extract|
|Source||Rhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス|
Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
|Map data||The map contains 120 Angstrom thick slab through the tube reconstruction.|
|Method||helical reconstruction, at 10.2 Å resolution|
|Authors||Korkhov VM / Sachse C / Short JM / Tate CG|
|Citation||Structure, 2010, 18, 677-687|
|Date||Deposition: Feb 5, 2010 / Header (metadata) release: Jun 24, 2010 / Map release: Jun 24, 2010 / Last update: Apr 13, 2016|
Downloads & links
|File||emd_1698.map.gz (map file in CCP4 format, 24416 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.2 Å|
CCP4 map header:
-Entire TspO and Escherichia coli polar lipid extract
|Entire||Name: TspO and Escherichia coli polar lipid extract / Number of components: 2 / Oligomeric State: Helical|
|Mass||Theoretical: 13.5 MDa / Experimental: 13.5 MDa|
-Component #1: protein, TspO
|Protein||Name: TspO / a.k.a: TspO / Oligomeric Details: Helical / Recombinant expression: Yes|
|Mass||Theoretical: 18 kDa / Experimental: 18 kDa|
|Source||Species: Rhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス|
|Source (engineered)||Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
|Source (natural)||Location in cell: Outer membrane|
-Component #2: cellular-component, Lipid extract
|Cellular-component||Name: Lipid extract / a.k.a: Lipid extract / Recombinant expression: No|
|Source||Species: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /|
|Specimen state||helical array|
|Helical parameters||Axial symmetry: D12 (2*12 fold dihedral) / Hand: LEFT HANDED / Delta z: 32 Å / Delta phi: 9.6 deg.|
|Crystal grow details||Incubated and dialysed for 3 days with Escherichia coli polar lipid extract|
|Sample solution||Specimen conc.: 0.5 mg/ml / Buffer solution: 20 mM Tris, 100 mM NaCl, 2 mM EDTA / pH: 7.5|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77.2 K / Method: Back-side blotting / Details: Vitrification instrument: Home built|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: May 30, 2007|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal)|
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2163 nm
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 36 / Scanner: OTHER / Sampling size: 6 microns / Bit depth: 8|
|Processing||Method: helical reconstruction|
Details: 2 TspO molecules within dimer are related by an additional 2-fold axis parallel to tube axis.
|3D reconstruction||Algorithm: Iterative algebraic reconstruction|
Euler angles: 2 degree increments, 0-360 degrees around helical axis, up to 12 degrees out-of-plane tilt
Software: SPIDER / CTF correction: Segment-specific CTF / Details: Imposition of 12-fold rotational symmetry / Resolution: 10.2 Å / Resolution method: FSC 0.5
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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