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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 data
SampleFljB
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.
Validation ReportSummary, Full report, XML, About validation report
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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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å
1.06 Å/pix.
x 400 pix.
= 424. Å
1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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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Segmentation: #1

Fileemd_0980_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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

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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

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Sample components

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Entire FljB

EntireName: FljB / Details: R-type straight flagellar filament (A461V) / Number of components: 1

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Component #1: protein, FljB

ProteinName: FljB / Details: R-type straight flagellar filament (A461V) / Recombinant expression: No
SourceSpecies: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SJW590

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Sample solutionpH: 7.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 10.3 e/Å2 / Illumination mode: OTHER
LensMagnification: 75000 X (nominal), 72273 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 2000.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2319

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 2319
3D reconstructionSoftware: RELION / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF

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