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- EMDB-5912: Cryo-electron tomography map of Leptospira interrogans flagellar motor -

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Basic information

Entry
Database: EMDB / ID: EMD-5912
TitleCryo-electron tomography map of Leptospira interrogans flagellar motor
Map dataReconstruction of Leptospira interrogans flagellar motor
Sample
  • Sample: Leptospira interrogans flagellar motor
  • Organelle or cellular component: FliY
Keywordsflagellar motor / C ring / stator / Leptospira interrogans
Biological speciesLeptospira interrogans (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 41.0 Å
AuthorsZhao XW / Norris SJ / Liu J
CitationJournal: J Bacteriol / Year: 2012
Title: Three-dimensional structures of pathogenic and saprophytic Leptospira species revealed by cryo-electron tomography.
Authors: Gianmarco Raddi / Dustin R Morado / Jie Yan / David A Haake / X Frank Yang / Jun Liu /
Abstract: Leptospira interrogans is the primary causative agent of the most widespread zoonotic disease, leptospirosis. An in-depth structural characterization of L. interrogans is needed to understand its ...Leptospira interrogans is the primary causative agent of the most widespread zoonotic disease, leptospirosis. An in-depth structural characterization of L. interrogans is needed to understand its biology and pathogenesis. In this study, cryo-electron tomography (cryo-ET) was used to compare pathogenic and saprophytic species and examine the unique morphological features of this group of bacteria. Specifically, our study revealed a structural difference between the cell envelopes of L. interrogans and Leptospira biflexa involving variations in the lipopolysaccharide (LPS) layer. Through cryo-ET and subvolume averaging, we determined the first three-dimensional (3-D) structure of the flagellar motor of leptospira, with novel features in the flagellar C ring, export apparatus, and stator. Together with direct visualization of chemoreceptor arrays, DNA packing, periplasmic filaments, spherical cytoplasmic bodies, and a unique "cap" at the cell end, this report provides structural insights into these fascinating Leptospira species.
History
DepositionFeb 24, 2014-
Header (metadata) releaseMar 12, 2014-
Map releaseApr 16, 2014-
UpdateSep 24, 2014-
Current statusSep 24, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5912.jpeg

emd_5912.tif

Downloads & links

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Map

FileDownload / File: emd_5912.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Leptospira interrogans flagellar motor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.7 Å/pix.
x 320 pix.
= 1824. Å		5.7 Å/pix.
x 320 pix.
= 1824. Å		5.7 Å/pix.
x 320 pix.
= 1824. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.77514762 - 0.84135616
Average (Standard dev.)0.0053047 (±0.04314546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 1824.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.75.75.7
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z1824.0001824.0001824.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.7750.8410.005

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Supplemental data

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Sample components

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Entire : Leptospira interrogans flagellar motor

EntireName: Leptospira interrogans flagellar motor
Components
  • Sample: Leptospira interrogans flagellar motor
  • Organelle or cellular component: FliY

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Supramolecule #1000: Leptospira interrogans flagellar motor

SupramoleculeName: Leptospira interrogans flagellar motor / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: FliY

SupramoleculeName: FliY / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Leptospira interrogans (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
DateMay 1, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -6.0 µm / Nominal defocus min: -4.0 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Details2 degree tilt angle incrememt
Final reconstructionResolution.type: BY AUTHOR / Resolution: 41.0 Å / Resolution method: OTHER / Software - Name: Protomo
Details: Final maps were calculated from 621 averaged datasets
Number subtomograms used: 61
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4fhr

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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