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Structural analysis of substrate binding by the TatBC component of the twin-arginine protein transport system.

by single particle reconstruction

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 20, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 20, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1634
TitleStructural analysis of substrate binding by the TatBC component of the twin-arginine protein transport system.
MapThis is a 3D map of a TatBC complex with one sufI substrate bound.
SampletatBC structure with one sufI substrate bound
Keywordstwin arginine, Tat, protein transport, blue native PAGE, single particle electron microscopy
AuthorsTarry MJ, Schaefer E, Chen S, Buchanan G, Greene NP, Lea SM, Palmer T, Saibil HR, Berks BC
DateDeposition: 2009-07-08, Header release: 2009-07-21, Map release: 2009-07-21, Last update: 2012-10-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 20, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 20, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 106, Issue 32, Page 13284-13289, Year 2009
TitleStructural analysis of substrate binding by the TatBC component of the twin-arginine protein transport system.
AuthorsMichael J Tarry, Eva Schäfer, Shuyun Chen, Grant Buchanan, Nicholas P Greene, Susan M Lea, Tracy Palmer, Helen R Saibil, Ben C Berks
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
KeywordsArginine (metabolism), Biological Transport, Escherichia coli (enzymology), Escherichia coli Proteins (chemistry), Membrane Transport Proteins (chemistry), Models, Molecular, Oxidoreductases (metabolism, 1.-), Substrate Specificity, SufI protein, E coli, TatB protein, E coli, TatC protein, E coli, cueO protein, E coli (1.-)
LinksPubMed: 19666509, DOI: 10.1073/pnas.0901566106, PMC: PMC2718047
Map
Fileemd_1634.map.gz ( map file in CCP4 format, 1025 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
5 A/pix
= 320. A
64 pix
5 A/pix
= 320. A
64 pix
5 A/pix
= 320. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:25 (by author), 20 (movie #1):
Minimum - Maximum: -90.8841 - 126.895
Average (Standard dev.): -2.25029 (10.0783)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
Unit CellA= B= C: 320 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 5 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z555
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z320.000320.000320.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-90.884126.895-2.250
Annotation DetailsThis is a 3D map of a TatBC complex with one sufI substrate bound.
Supplement
Images
Images
Sample
NametatBC structure with one sufI substrate bound
Number of Components3
Component #1: protein - tat
Scientific nametwin arginine transporter
Common Nametat
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionYes
Experiment
Sample Preparation
Stainingnegatively stained with 2% (wt/vol) uranyl acetate on glow discharged, continuous carbon-coated 300 mesh copper grids (Agar Scientific).
Specimen Support Details300
Specimen Stateparticle
BufferpH: 0.014
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage120 kV
Illumination ModeOTHER
Lens
MagnificationNominal: 42000
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 2000 nm
Specimen Holder
Holdereucentric
ModelOTHER
Tilt Angle0 degrees - 50 degrees
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerZEISS SCAI
Sampling Size7
DetailsMicrographs 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.
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareSPIDER
DetailsThe 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.
Single Particle
Number of Projections1556
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1634.xml (6.8 KB)
Map dataemd_1634.map.gz (40.4 KB)
ImagesEMD-1634.gif (26.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1634
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 25.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 26.3 KB