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- EMDB-25123: Focused refinement structure of Helicobacter pylori flagellar motor -

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Basic information

Entry
Database: EMDB / ID: EMD-25123
TitleFocused refinement structure of Helicobacter pylori flagellar motor
Map dataThe focused refinement structure of wild type H. pylori flagella motor.
Sample
  • Organelle or cellular component: Helicobacter pylori flagellar motor
Biological speciesHelicobacter pylori SS1 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 24.0 Å
AuthorsLiu J / Tachiyama S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation.
Authors: Shoichi Tachiyama / Kar L Chan / Xiaolin Liu / Skander Hathroubi / Briana Peterson / Mohammad F Khan / Karen M Ottemann / Jun Liu / Anna Roujeinikova /
Abstract: The flagellar motor stator is an ion channel nanomachine that assembles as a ring of the MotAMotB units at the flagellar base. The role of accessory proteins required for stator assembly and ...The flagellar motor stator is an ion channel nanomachine that assembles as a ring of the MotAMotB units at the flagellar base. The role of accessory proteins required for stator assembly and activation remains largely enigmatic. Here, we show that one such assembly factor, the conserved protein FliL, forms an integral part of the flagellar motor in a position that colocalizes with the stator. Cryogenic electron tomography reconstructions of the intact motor in whole wild-type cells and cells lacking FliL revealed that the periplasmic domain of FliL (FliL-C) forms 18 circumferentially positioned rings integrated with the 18 MotAB units. FliL-C formed partial rings in the crystal, and the crystal structure-based full ring model was consistent with the shape of the rings observed in situ. Our data suggest that each FliL ring is coaxially sandwiched between the MotA ring and the dimeric periplasmic MotB moiety of the stator unit and that the central hole of the FliL ring has density that is consistent with the plug/linker region of MotB in its extended, active conformation. Significant structural similarities were found between FliL-C and stomatin/prohibitin/flotillin/HflK/C domains of scaffolding proteins, suggesting that FliL acts as a scaffold. The binding energy released upon association of FliL with the stator units could be used to power the release of the plug helices. The finding that isolated FliL-C forms stable partial rings provides an insight into the putative mechanism by which the FliL rings assemble around the stator units.
History
DepositionOct 8, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateFeb 2, 2022-
Current statusFeb 2, 2022Processing 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
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  • 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_25123.png

Downloads & links

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Map

FileDownload / File: emd_25123.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe focused refinement structure of wild type H. pylori flagella motor.
Voxel sizeX=Y=Z: 4.4 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.32737094 - 0.42594522
Average (Standard dev.)6.2482325e-11 (±0.0722672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.44.44.4
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z528.000528.000528.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-0.3270.4260.000

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Supplemental data

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Sample components

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Entire : Helicobacter pylori flagellar motor

EntireName: Helicobacter pylori flagellar motor
Components
  • Organelle or cellular component: Helicobacter pylori flagellar motor

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Supramolecule #1: Helicobacter pylori flagellar motor

SupramoleculeName: Helicobacter pylori flagellar motor / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Helicobacter pylori SS1 (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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C18 (18 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 14148
ExtractionNumber tomograms: 95 / Number images used: 786
Final angle assignmentType: OTHER

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