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- EMDB-1698: Three-dimensional structure of TspO by electron cryo-microscopy o... -

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Basic information

Entry
Database: EMDB / ID: 1698
TitleThree-dimensional structure of TspO by electron cryo-microscopy of helical crystals.
KeywordsTSPO / PBR / membrane protein / helical crystal
SampleTspO and Escherichia coli polar lipid extract
SourceRhodobacter 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 dataThe map contains 120 Angstrom thick slab through the tube reconstruction.
Methodhelical reconstruction, at 10.2 Å resolution
AuthorsKorkhov VM / Sachse C / Short JM / Tate CG
CitationStructure, 2010, 18, 677-687

Structure, 2010, 18, 677-687 StrPapers
Three-dimensional structure of TspO by electron cryomicroscopy of helical crystals.
Vladimir M Korkhov / Carsten Sachse / Judith M Short / Christopher G Tate

DateDeposition: Feb 5, 2010 / Header (metadata) release: Jun 24, 2010 / Map release: Jun 24, 2010 / Last update: Apr 13, 2016

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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
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Slabnear <=> far

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Supplemental images

Downloads & links

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Map

Fileemd_1698.map.gz (map file in CCP4 format, 24416 KB)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
1.2 Å/pix.
= 120. Å
250 pix
1.2 Å/pix.
= 300. Å
250 pix
1.2 Å/pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.2 Å
Density
Contour Level:1.75 (by author), 1.75 (movie #1):
Minimum - Maximum-2.11997 - 3.8827
Average (Standard dev.)5.7552e-09 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250100
Origin-125-125-50
Limit12412449
Spacing250250100
CellA: 300 Å / B: 300 Å / C: 120 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-125-125-50
NC/NR/NS250250100
D min/max/mean-2.1203.8830.000

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Supplemental data

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Sample components

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Entire TspO and Escherichia coli polar lipid extract

EntireName: TspO and Escherichia coli polar lipid extract / Number of components: 2 / Oligomeric State: Helical
MassTheoretical: 13.5 MDa / Experimental: 13.5 MDa

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Component #1: protein, TspO

ProteinName: TspO / a.k.a: TspO / Oligomeric Details: Helical / Recombinant expression: Yes
MassTheoretical: 18 kDa / Experimental: 18 kDa
SourceSpecies: 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 /
Vector: pUI2701
Source (natural)Location in cell: Outer membrane

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Component #2: cellular-component, Lipid extract

Cellular-componentName: Lipid extract / a.k.a: Lipid extract / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen statehelical array
Helical parametersAxial symmetry: D12 (2*12 fold dihedral) / Hand: LEFT HANDED / Delta z: 32 Å / Delta phi: 9.6 deg.
Crystal grow detailsIncubated and dialysed for 3 days with Escherichia coli polar lipid extract
Sample solutionSpecimen conc.: 0.5 mg/ml / Buffer solution: 20 mM Tris, 100 mM NaCl, 2 mM EDTA / pH: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77.2 K / Method: Back-side blotting / Details: Vitrification instrument: Home built

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: May 30, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 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 HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 36 / Scanner: OTHER / Sampling size: 6 microns / Bit depth: 8

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Image processing

ProcessingMethod: helical reconstruction
Details: 2 TspO molecules within dimer are related by an additional 2-fold axis parallel to tube axis.
3D reconstructionAlgorithm: 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

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