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- EMDB-0980: CryoEM structure of S.typhimurium R-type straight flagellar filam... -

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Basic information

Entry
Database: EMDB / ID: EMD-0980
TitleCryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V)
Map dataCryo-EM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V) .
Sample
  • Complex: FljB
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsYamaguchi T / Toma S
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biomolecules / Year: 2020
Title: Structural and Functional Comparison of Flagellar Filaments Composed of FljB and FliC.
Authors: Tomoko Yamaguchi / Shoko Toma / Naoya Terahara / Tomoko Miyata / Masamichi Ashihara / Tohru Minamino / Keiichi Namba / Takayuki Kato /
Abstract: The bacterial flagellum is a motility organelle consisting of a long helical filament as a propeller and a rotary motor that drives rapid filament rotation to produce thrust. serovar Typhimurium has ...The bacterial flagellum is a motility organelle consisting of a long helical filament as a propeller and a rotary motor that drives rapid filament rotation to produce thrust. serovar Typhimurium has two genes of flagellin, and , for flagellar filament formation and autonomously switches their expression at a frequency of 10-10 per cell per generation. We report here differences in their structures and motility functions under high-viscosity conditions. A strain expressing FljB showed a higher motility than one expressing FliC under high viscosity. To examine the reasons for this motility difference, we carried out structural analyses of the FljB filament by electron cryomicroscopy and found that the structure was nearly identical to that of the FliC filament except for the position and orientation of the outermost domain D3 of flagellin. The density of domain D3 was much lower in FljB than FliC, suggesting that domain D3 of FljB is more flexible and mobile than that of FliC. These differences suggest that domain D3 plays an important role not only in changing antigenicity of the filament but also in optimizing motility function of the filament as a propeller under different conditions.
History
DepositionJan 29, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0980.png

Downloads & links

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Map

FileDownload / File: emd_0980.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V) .
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.026757246 - 0.0648524
Average (Standard dev.)0.0007916083 (±0.004393688)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-199-199-199
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS-199-199-199
NC/NR/NS400400400
D min/max/mean-0.0270.0650.001

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Supplemental data

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Mask #1

Fileemd_0980_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map 1 of 3D Refinement.

Fileemd_0980_half_map_1.map
AnnotationCryo-EM half map 1 of 3D Refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map 2 of 3D Refinement.

Fileemd_0980_half_map_2.map
AnnotationCryo-EM half map 2 of 3D Refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FljB

EntireName: FljB
Components
  • Complex: FljB

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Supramolecule #1: FljB

SupramoleculeName: FljB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: R-type straight flagellar filament (A461V)
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SJW590

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTristris (hydroxymethyl) amino methane
150.0 mMNaClSodium chlorideSodium chloride
1.0 mMMgCl2Magnesium Chloride
Sugar embeddingMaterial: buffer
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.6 µm / Calibrated defocus min: 0.21 µm / Calibrated magnification: 72273 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-6 / Number grids imaged: 3 / Number real images: 2319 / Average electron dose: 10.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 197442
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER / Details: CryoEM map of FliC flagellar filament
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0) / Software - details: beta-2
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0 beta-2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 beta2) / Number images used: 2319

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