EMDB-2158: Bacterial chemoreceptor arrays are hexagonally packed ...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 2158
Authors	Briegel A, Li X, Bilwes AM, Hughes KT, Jensen GJ, Crane BR
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 164, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 164, Made by UCSF CHIMERA
Supplemental images	EMD-2158.png
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)	Diagram EMDB-5189 PDB-3j3b EMDB-1528 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 10, Page 3766-71, Year 2012
Title	Bacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins.
Authors	Ariane Briegel, Xiaoxiao Li, Alexandrine M Bilwes, Kelly T Hughes, Grant J Jensen, Brian R Crane Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
Keywords	Bacillus subtilis (metabolism), Bacterial Physiological Phenomena, Bacterial Proteins (chemistry), CheW protein, E coli, Chemoreceptor Cells (cytology), Chemotaxis, Crystallization, Crystallography, X-Ray (methods), Cytoplasm (metabolism), Dimerization, Electron Microscope Tomography (methods), Escherichia coli (metabolism), Escherichia coli Proteins (chemistry), Membrane Proteins (chemistry), Protein Binding, Protein Conformation, Salmonella enterica (metabolism), methyl-accepting chemotaxis proteins
Links	DOI: 10.1073/pnas.1115719109, PubMed: 22355139, PMC: PMC3309718

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 233.28 A , B = 233.28 A , C = 388.8 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 6.48 A , Y = 6.48 A , Z = 6.48 A

CCP4 map header info

Annotation Details

3-fold average of wild-type E.coli (strain RP437) Chemoreceptor array sub-volumes (composed of 6 trimers-of receptor dimers)

Sample
Name	Bacterial chemoreceptor arrays
Number of Components	3
Oligomeric State	Trimers of receptor dimers lie at the vertices of a hexagonal lattice in a two-facing-two configuration surrounding a ring of alternating CheA regulatory domains (P5) and CheW couplers
Component #1: protein - cheA
Scientific name	cheA
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Strain	MG1655
Recombinant expression	No
Natural Source	Cell Location: Inner membrane
Component #2: protein - cheW
Scientific name	cheW
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Strain	MG1655
Recombinant expression	No
Natural Source	Cell Location: Inner membrane
Component #3: protein - Chemoreceptors
Scientific name	Chemoreceptors
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Strain	MG1655
Recombinant expression	No
Natural Source	Cell Location: Inner membrane

Experiment
Sample Preparation
Specimen Support Details	R 2/2 copper/Rhodium grids, glow discharged
Buffer	Details: Tryptone Broth (10 g Tryptone, 5 g NaCl per liter). Cells were grown to exponential phase and incubated with penicillin for 1 hour prior to freezing
Vitrification
Cryogen Name	ETHANE
Humidity	100
Instrument	FEI VITROBOT MARK III
Imaging
Microscope	FEI POLARA 300
Date	15-JAN-2008
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	150 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 34000 X,
Nominal Cs	2.2 mm
Imaging Mode	BRIGHT FIELD
Defocus	10000 nm -
Energy Filter	Type: Gif 2002 hybrid (Gatan) , Window: 0-20 eV
Specimen Holder
Holder	( OTHER )
Tilt Angle	-70 degrees - 58 degrees
Temperature	77 Kelvin
Camera
Detector	4kx4k Ultracam (Gatan)
Image Acquisition

Processing
Method	subtomogram averaging
3 D reconstruction
Software	imod
CTF Correction	imod
Subtomogram Averaging
Details	CTF correction in imod. Average number of tilts used in the 3D reconstructions: 130. Average tomographic tilt angle increment: 1.
Atomic Model Fitting
Model #0
Details	Protocol: rigid body
Refinement Protocol	rigid body
Refinement Space	REAL

Data from EMDB

Header (meta data in XML format)

Map data

Images

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.8 MB Session file for UCSF-Chimera, 26.7 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3 MB .webm (WebM/VP8 format), 4.2 MB Session file for UCSF-Chimera, 26.7 KB