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- EMDB-1634: Structural analysis of substrate binding by the TatBC component o... -

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Basic information

Entry
Database: EMDB / ID: 1634
TitleStructural analysis of substrate binding by the TatBC component of the twin-arginine protein transport system.
Map dataThis is a 3D map of a TatBC complex with one sufI substrate bound.
SampletatBC structure with one sufI substrate bound:
twin arginine transporter
Keywordstwin arginine / Tat / protein transport / blue native PAGE / single particle electron microscopy
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining
AuthorsTarry MJ / Schaefer E / Chen S / Buchanan G / Greene NP / Lea SM / Palmer T / Saibil HR / Berks BC
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2009
Title: Structural analysis of substrate binding by the TatBC component of the twin-arginine protein transport system.
Authors: Michael J Tarry / Eva Schäfer / Shuyun Chen / Grant Buchanan / Nicholas P Greene / Susan M Lea / Tracy Palmer / Helen R Saibil / Ben C Berks
DateDeposition: Jul 8, 2009 / Header (metadata) release: Jul 21, 2009 / Map release: Jul 21, 2009 / Last update: Oct 10, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 20
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 20
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1634.map.gz (map file in CCP4 format, 1025 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
5 Å/pix.
= 320. Å
64 pix
5 Å/pix.
= 320. Å
64 pix
5 Å/pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5 Å
Density
Contour Level:25 (by author), 20 (movie #1):
Minimum - Maximum-90.8841 - 126.895
Average (Standard dev.)-2.25029 (10.0783)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 320 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z555
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z320.000320.000320.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-90.884126.895-2.250

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Supplemental data

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Sample components

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Entire tatBC structure with one sufI substrate bound

EntireName: tatBC structure with one sufI substrate bound / Number of components: 3

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Component #1: protein, twin arginine transporter

ProteinName: twin arginine transporter / a.k.a: tat / Recombinant expression: Yes
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionpH: 0.014
Support film300
Stainingnegatively stained with 2% (wt/vol) uranyl acetate on glow discharged, continuous carbon-coated 300 mesh copper grids (Agar Scientific).
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Illumination mode: OTHER
LensMagnification: 42000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 2000 nm
Specimen HolderHolder: eucentric / Model: OTHER / Tilt Angle: 0 - 50 deg.
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 7 microns
Details: Micrographs were digitized on a Zeiss SCAI scanner at a pixel size of 7 micron, corresponding to 1.667 angstroms on the specimen. Subsequently, adjacent pixels were 3 x 3 averaged to yield a pixel size of 5 angstroms.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1556 / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: SPIDER
Details: The tilted images were corrected for the effects of the contrast transfer function (CTF) by phase flipping, taking into account the defocus gradient across the micrographs and the position of each particle. Images were processed using SPIDER version 11.12 and 15.06. Three-dimensional reconstruction was performed by the random conical tilt method in SPIDER. The particles were windowed into 64 x 64 pixel boxes.

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