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- EMDB-8459: Structure of Helicobacter pylori flagellar motor in situ by cryo-... -

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Basic information

Entry
Database: EMDB / ID: EMD-8459
TitleStructure of Helicobacter pylori flagellar motor in situ by cryo-electron tomography
Map dataAveraged map of Helicobacter pylori flagellar motor in situ from motors with flagella, C6-symmetrized
Sample
  • Organelle or cellular component: Helicobacter pylori flagellar motor in situ from motors with flagella, C6-symmetrized
Biological speciesHelicobacter pylori (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsQin Z / Liu J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institute of Allergy and Infections DiseasesR01AI087946 United States
Welch FoundationAU-1714 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107629 United States
CitationJournal: J Bacteriol / Year: 2017
Title: Imaging the motility and chemotaxis machineries in Helicobacter pylori by cryo-electron tomography.
Authors: Zhuan Qin / Wei-Ting Lin / Shiwei Zhu / Aime T Franco / Jun Liu /
Abstract: Helicobacter pylori is a bacterial pathogen that can cause many gastrointestinal diseases including ulcers and gastric cancer. A unique chemotaxis-mediated motility is critical for H. pylori to ...Helicobacter pylori is a bacterial pathogen that can cause many gastrointestinal diseases including ulcers and gastric cancer. A unique chemotaxis-mediated motility is critical for H. pylori to colonize in the human stomach and to establish chronic infection, but the underlying molecular mechanisms are not well understood. Here we employ cryo-electron tomography to reveal detailed structures of the H. pylori cell envelope including the sheathed flagella and chemotaxis arrays. Notably, H. pylori possesses a distinctive periplasmic cage-like structure with 18-fold symmetry. We propose that this structure forms a robust platform for recruiting 18 torque generators, which likely provide the higher torque needed for swimming in high-viscosity environments. We also reveal a series of key flagellar assembly intermediates, providing structural evidence that flagellar assembly is tightly coupled with biogenesis of the membrane sheath. Finally, we determine the structure of putative chemotaxis arrays at the flagellar pole, which have implications for how direction of flagellar rotation is regulated. Together, our pilot cryo-ET studies provide novel structural insights into the unipolar flagella of H. pylori and lay a foundation for a better understanding of the unique motility of this organism.
IMPORTANCE: Helicobacter pylori is a highly motile bacterial pathogen that colonizes approximately 50% of the world's population. H. pylori can move readily within the viscous mucosal layer of the ...IMPORTANCE: Helicobacter pylori is a highly motile bacterial pathogen that colonizes approximately 50% of the world's population. H. pylori can move readily within the viscous mucosal layer of the stomach. It has become increasingly clear that its unique flagella-driven motility is essential for successful gastric colonization and pathogenesis. Here we use advanced imaging techniques to visualize novel in situ structures with unprecedented detail in intact H. pylori cells. Remarkably, H. pylori possesses multiple unipolar flagella, which are driven by one of the largest flagellar motors found in bacteria. These large motors presumably provide higher torque needed by the bacterial pathogens to navigate in viscous environment of the human stomach.
History
DepositionOct 28, 2016-
Header (metadata) releaseNov 30, 2016-
Map releaseNov 30, 2016-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8459_1.png

emd_8459_2.png

Downloads & links

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Map

FileDownload / File: emd_8459.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged map of Helicobacter pylori flagellar motor in situ from motors with flagella, C6-symmetrized
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.45 Å/pix.
x 240 pix.
= 1068.48 Å		4.45 Å/pix.
x 240 pix.
= 1068.48 Å		4.45 Å/pix.
x 240 pix.
= 1068.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.452 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.26332682 - 0.37178853
Average (Standard dev.)0.00022168299 (±0.048428155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 1068.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.4524.4524.452
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z1068.4801068.4801068.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-0.2630.3720.000

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Supplemental data

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Additional map: Averaged map of Helicobacter pylori flagellar motor in...

Fileemd_8459_additional.map
AnnotationAveraged map of Helicobacter pylori flagellar motor in situ from motors without flagella, C6-symmetrized
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helicobacter pylori flagellar motor in situ from motors with flag...

EntireName: Helicobacter pylori flagellar motor in situ from motors with flagella, C6-symmetrized
Components
  • Organelle or cellular component: Helicobacter pylori flagellar motor in situ from motors with flagella, C6-symmetrized

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Supramolecule #1: Helicobacter pylori flagellar motor in situ from motors with flag...

SupramoleculeName: Helicobacter pylori flagellar motor in situ from motors with flagella, C6-symmetrized
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: wild-type
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: 7.13

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6
GridMaterial: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 363
ExtractionNumber tomograms: 100 / Number images used: 363 / Software - Name: IMOD
Final angle assignmentType: OTHER

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Atomic model buiding 1

RefinementProtocol: OTHER

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