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

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Basic information

Entry
Database: EMDB / ID: EMD-2158
TitleBacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins
Map data3-fold average of wild-type E.coli (strain RP437) Chemoreceptor array sub-volumes (composed of 6 trimers-of receptor dimers)
Sample
  • Sample: Bacterial chemoreceptor arrays
  • Protein or peptide: cheA
  • Protein or peptide: cheW
  • Protein or peptide: Chemoreceptors
Keywordschemotaxis / signal transduction / two-component systems
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM
AuthorsBriegel A / Li X / Bilwes AM / Hughes KT / Jensen GJ / Crane BR
CitationJournal: Proc Natl Acad Sci U S A / 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 /
Abstract: Chemoreceptor arrays are supramolecular transmembrane machines of unknown structure that allow bacteria to sense their surroundings and respond by chemotaxis. We have combined X-ray crystallography ...Chemoreceptor arrays are supramolecular transmembrane machines of unknown structure that allow bacteria to sense their surroundings and respond by chemotaxis. We have combined X-ray crystallography of purified proteins with electron cryotomography of native arrays inside cells to reveal the arrangement of the component transmembrane receptors, histidine kinases (CheA) and CheW coupling proteins. 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. Whereas the CheA kinase domains (P4) project downward below the ring, the CheA dimerization domains (P3) link neighboring rings to form an extended, stable array. This highly interconnected protein architecture underlies the remarkable sensitivity and cooperative nature of transmembrane signaling in bacterial chemotaxis.
History
DepositionJul 6, 2012-
Header (metadata) releaseJul 25, 2012-
Map releaseJul 25, 2012-
UpdateAug 1, 2012-
Current statusAug 1, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 164
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 164
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2158.png

Downloads & links

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Map

FileDownload / File: emd_2158.map.gz / Format: CCP4 / Size: 297.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3-fold average of wild-type E.coli (strain RP437) Chemoreceptor array sub-volumes (composed of 6 trimers-of receptor dimers)
Voxel sizeX=Y=Z: 6.48 Å
Density
Contour LevelBy AUTHOR: 164.0 / Movie #1: 164
Minimum - Maximum155.039993290000012 - 168.389999390000014
Average (Standard dev.)161.905410770000003 (±1.43633509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions363660
Spacing363660
CellA: 233.28 Å / B: 233.28 Å / C: 388.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.486.486.48
M x/y/z363660
origin x/y/z0.0000.0000.000
length x/y/z233.280233.280388.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS363660
D min/max/mean155.040168.390161.905

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Supplemental data

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Sample components

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Entire : Bacterial chemoreceptor arrays

EntireName: Bacterial chemoreceptor arrays
Components
  • Sample: Bacterial chemoreceptor arrays
  • Protein or peptide: cheA
  • Protein or peptide: cheW
  • Protein or peptide: Chemoreceptors

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Supramolecule #1000: Bacterial chemoreceptor arrays

SupramoleculeName: Bacterial chemoreceptor arrays / type: sample / ID: 1000
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
Number unique components: 3

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Macromolecule #1: cheA

MacromoleculeName: cheA / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655 / Location in cell: Inner membrane

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Macromolecule #2: cheW

MacromoleculeName: cheW / type: protein_or_peptide / ID: 2 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655 / Location in cell: Inner membrane

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Macromolecule #3: Chemoreceptors

MacromoleculeName: Chemoreceptors / type: protein_or_peptide / ID: 3 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655 / Location in cell: Inner membrane

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferDetails: 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
GridDetails: R 2/2 copper/Rhodium grids, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus min: 10.0 µm / Nominal magnification: 34000
Specialist opticsEnergy filter - Name: Gif 2002 hybrid (Gatan) / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: OTHER / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 58 °
TemperatureAverage: 77 K
DateJan 15, 2008
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 150 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: imod
Final reconstructionSoftware - Name: imod
DetailsCTF correction in imod. Average number of tilts used in the 3D reconstructions: 130. Average tomographic tilt angle increment: 1.

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Atomic model buiding 1

Initial modelPDB ID:

3ur1


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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