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Three-dimensional structure of TspO by electron cryo-microscopy of helical crystals.

by helical reconstruction, at 10.2 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.75, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.75, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1698
TitleThree-dimensional structure of TspO by electron cryo-microscopy of helical crystals.
MapThe map contains 120 Angstrom thick slab through the tube reconstruction.
SampleTspO and Escherichia coli polar lipid extract
KeywordsTSPO, PBR, membrane protein, helical crystal
AuthorsKorkhov VM, Sachse C, Short JM, Tate CG
DateDeposition: 2010-02-05, Header release: 2010-06-24, Map release: 2010-06-24, Last update: 2010-06-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.75, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.75, Made by UCSF CHIMERA

Supplemental images

1698.tif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
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Diagram

PDB-3h3y
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleStructure, Vol. 18, Issue 6, Page 677-87, Year 2010
TitleThree-dimensional structure of TspO by electron cryomicroscopy of helical crystals.
AuthorsVladimir M Korkhov, Carsten Sachse, Judith M Short, Christopher G Tate
Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. <>
KeywordsCryoelectron Microscopy (methods), Detergents, Membrane Proteins (chemistry), Mitochondrial Membranes (metabolism), Protein Structure, Secondary, Rhodobacter sphaeroides (metabolism)
LinksPII: S0969-2126(10)00107-3, DOI: 10.1016/j.str.2010.03.001, PubMed: 20541505, PMC: PMC2911597
Map
FileEMD-1698.map ( map file in CCP4 format, 25002 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:1.75 (by author), 1.75 (movie #1):
Minimum - Maximum: -2.11997 - 3.8827
Average (Standard dev.): 5.7552e-09 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 250 250 100
Origin : -125 -125 -50
Limit : 124 124 49
Spacing : 250 250 100
Unit CellA = 300 A , B = 300 A , C = 120 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 1.2 A , Y = 1.2 A , Z = 1.2 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-125-125-50
NC/NR/NS250250100
start NC,NX/NR,NY/NS,NZ-125-125-50
NC,NX/NR,NY/NS,NZ250250100
D min/max/mean-2.1203.8830.000
Annotation DetailsThe map contains 120 Angstrom thick slab through the tube reconstruction.
Supplement
Images
Images

1698.tif
Sample
NameTspO and Escherichia coli polar lipid extract
Number of Components2
Oligomeric StateHelical
Theoretical Mass13.5 MDa
Experimental Mass13.5 MDa
Component #1: protein - TspO
Scientific nameTspO
Theoretical Mass0.018 MDa
Experimental Mass0.018 MDa
Oligomeric DetailsHelical
Scientific Name of SpeciesRhodobacter sphaeroides (NCBI Taxonomy: 1063)
Common Name of SpeciesRhodobacter sphaeroides
Recombinant expressionYes
Natural SourceCell Location: Outer membrane
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Vector: pUI2701
Component #2: cellular-component - Lipid extract
Scientific nameLipid extract
Scientific Name of SpeciesEscherichia coli (NCBI Taxonomy: 562)

Recombinant expressionNo
Experiment
Sample Preparation
Helical ParametersAxial Symmetry: s12
Delta Z: 32 A
Delta Phi: 9.6 degrees
Hand: LEFT HANDED
Specimen Conc0.5 mg/ml
Specimen StatehelicalArray
Crystal Grow DetailsIncubated and dialysed for 3 days with Escherichia coli polar lipid extract
BufferpH: 7.5
Details: 20 mM Tris, 100 mM NaCl, 2 mM EDTA
Vitrification
MethodBack-side blotting
Cryogen NameETHANE
DetailsVitrification instrument: Home built
InstrumentHOMEMADE PLUNGER
Temperature77.2 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Date30-MAY-2007
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X,
AstigmatismObjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 2163 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder ( GATAN LIQUID NITROGEN )
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerOTHER
Number of Digital Images36
Sampling Size6 microns
Quant Bit Number8
Processing
Methodhelical reconstruction
3 D reconstruction
AlgorithmIterative algebraic reconstruction
Euler Angles Details2 degree increments, 0-360 degrees around helical axis, up to 12 degrees out-of-plane tilt
SoftwareSPIDER
CTF CorrectionSegment-specific CTF
DetailsImposition of 12-fold rotational symmetry
Resolution By Author10.2
Resolution MethodFSC at 0.5 cut-off
Helical
Details2 TspO molecules within dimer are related by an additional 2-fold axis parallel to tube axis.
Download
Data from EMDB
Header (meta data in XML format)emd-1698.xml (8.5 KB)
Map dataemd_1698.map.gz (21.8 MB)
Images1698.tif (909.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1698
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.2 KB