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- EMDB-1235: In situ structure of the complete Treponema primitia flagellar motor. -

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Basic information

Entry
Database: EMDB / ID: EMD-1235
TitleIn situ structure of the complete Treponema primitia flagellar motor.
Map dataSee header. As submitted, low values correspond to protein density, and it should be contoured at 1.3 standard deviations.
Sample
  • Sample: Flagellar MotorFlagellum
  • Organelle or cellular component: Flagellar MotorFlagellum
Biological speciesTreponema primitia (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 70.0 Å
AuthorsMurphy GE / Leadbetter JR / Jensen GJ
CitationJournal: Nature / Year: 2006
Title: In situ structure of the complete Treponema primitia flagellar motor.
Authors: Gavin E Murphy / Jared R Leadbetter / Grant J Jensen /
Abstract: The bacterial flagellar motor is an amazing nanomachine: built from approximately 25 different proteins, it uses an electrochemical ion gradient to drive rotation at speeds of up to 300 Hz (refs 1, 2) ...The bacterial flagellar motor is an amazing nanomachine: built from approximately 25 different proteins, it uses an electrochemical ion gradient to drive rotation at speeds of up to 300 Hz (refs 1, 2). The flagellar motor consists of a fixed, membrane-embedded, torque-generating stator and a typically bidirectional, spinning rotor that changes direction in response to chemotactic signals. Most structural analyses so far have targeted the purified rotor, and hence little is known about the stator and its interactions. Here we show, using electron cryotomography of whole cells, the in situ structure of the complete flagellar motor from the spirochaete Treponema primitia at 7 nm resolution. Twenty individual motor particles were computationally extracted from the reconstructions, aligned and then averaged. The stator assembly, revealed for the first time, possessed 16-fold symmetry and was connected directly to the rotor, C ring and a novel P-ring-like structure. The unusually large size of the motor suggested mechanisms for increasing torque and supported models wherein critical interactions occur atop the C ring, where our data suggest that both the carboxy-terminal and middle domains of FliG are found.
History
DepositionApr 6, 2006-
Header (metadata) releaseJul 6, 2006-
Map releaseAug 4, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1235.gif

Downloads & links

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Map

FileDownload / File: emd_1235.map.gz / Format: CCP4 / Size: 335.9 KB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationSee header. As submitted, low values correspond to protein density, and it should be contoured at 1.3 standard deviations.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
19.6 Å/pix.
x 56 pix.
= 1097.6 Å		19.6 Å/pix.
x 56 pix.
= 1097.6 Å		19.6 Å/pix.
x 56 pix.
= 1097.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 19.6 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 11.0 / Movie #1: 10.5
Minimum - Maximum-39.0 - 61.0
Average (Standard dev.)-0.0815188 (±6.92315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-28-28-28
Dimensions565656
Spacing565656
CellA=B=C: 1097.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z19.619.619.6
M x/y/z565656
origin x/y/z0.0000.0000.000
length x/y/z1097.6001097.6001097.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-28-28-28
NC/NR/NS565656
D min/max/mean-39.00061.000-0.082

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Supplemental data

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Sample components

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Entire : Flagellar Motor

EntireName: Flagellar MotorFlagellum
Components
  • Sample: Flagellar MotorFlagellum
  • Organelle or cellular component: Flagellar MotorFlagellum

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Supramolecule #1000: Flagellar Motor

SupramoleculeName: Flagellar Motor / type: sample / ID: 1000
Details: The flagellar motor is built from more than 20 proteins, some of which are unknown. The stoichiometry is not certain.
Number unique components: 1

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Supramolecule #1: Flagellar Motor

SupramoleculeName: Flagellar Motor / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Basal Body
Details: tens of megadaltons; T. primitia is a spirochete with a periplasmic flagella. It never exits the outer membrane.
Recombinant expression: No / Database: NCBI
Source (natural)Organism: Treponema primitia (bacteria) / Cell: Treponema primitia strain ZAS-2 / Location in cell: Plasma membrane

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferDetails: T. primitia cells were frozen in their 4YACo growth media (Leadbetter et al., Science 1999)
GridDetails: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot
Method: Typically a 2 second blot, -2 offset and a 1 s drain.

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal magnification: 22500
Specialist opticsEnergy filter - Name: GIF 3000 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: FEI Polara / Specimen holder model: GATAN HELIUM / Tilt series - Axis1 - Min angle: 63 ° / Tilt series - Axis1 - Max angle: 63 °
TemperatureMin: 82 K / Max: 82 K / Average: 82 K
Alignment procedureLegacy - Astigmatism: obj lens astigmatism corrected at working magnification
Legacy - Electron beam tilt params: 0
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 110 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: none
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 70.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD
Details: Final map is the C16 symmetrized average calculated from 20 individual 3D motor particles.
DetailsMotor particles were picked from 15 different tomograms. The above parameters are the typical values. Average number of tilts used in the 3D reconstructions: 125. Average tomographic tilt angle increment: 1.

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