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- EMDB-9896: CryoEM structure of S.typhimurium R-type flagellar filament made ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9896
TitleCryoEM structure of S.typhimurium R-type flagellar filament made of FljB (A461V) without domain D3 by masking out
Map dataCryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V)
Sample
  • Complex: FljB
    • Protein or peptide: Flagellin
KeywordsFljB / Helical reconstruction / Salmonella / Flagellar motor / PROTEIN FIBRIL
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodhelical 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
DepositionApr 25, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jy0
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jy0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9896.png

Downloads & links

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Map

FileDownload / File: emd_9896.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V)
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.10676585 - 0.16655359
Average (Standard dev.)0.0005601356 (±0.009007921)
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/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-199-199-199
NC/NR/NS400400400
D min/max/mean-0.1070.1670.001

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Supplemental data

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Mask #1

Fileemd_9896_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_9896_half_map_1.map
AnnotationEM half map-1 of 3D Refinement CryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_9896_half_map_2.map
AnnotationEM half map-2 of 3D Refinement CryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V)
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
    • Protein or peptide: Flagellin

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Supramolecule #1: FljB

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

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 52.608449 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
SequenceString: MAQVINTNSL SLLTQNNLNK SQSALGTAIE RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQASRNAND GISIAQTTEG ALNEINNNL QRVRELAVQS ANSTNSQSDL DSIQAEITQR LNEIDRVSGQ TQFNGVKVLA QDNTLTIQVG ANDGETIDID L KQINSQTL ...String:
MAQVINTNSL SLLTQNNLNK SQSALGTAIE RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQASRNAND GISIAQTTEG ALNEINNNL QRVRELAVQS ANSTNSQSDL DSIQAEITQR LNEIDRVSGQ TQFNGVKVLA QDNTLTIQVG ANDGETIDID L KQINSQTL GLDSLNVQKA YDVKDTAVTT KAYANNGTTL DVSGLDDAAI KAATGGTNGT ASVTGGAVKF DADNNKYFVT IG GFTGADA AKNGDYEVNV ATDGTVTLAA GATKTTMPAG ATTKTEVQEL KDTPAVVSAD AKNALIAGGV DATDANGAEL VKM SYTDKN GKTIEGGYAL KAGDKYYAAD YDEATGAIKA KTTSYTAADG TTKTAANQLG GVDGKTEVVT IDGKTYNASK AAGH DFKAQ PELAEAAAKT TENPLQKIDA ALAQVDALRS DLGAVQNRFN SAITNLGNTV NNLSEVRSRI EDSDYATEVS NMSRA QILQ QAGTSVLAQA NQVPQNVLSL LR

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMTris-HCltris (hydroxymethyl) amino methane
150.0 mMNaClSodium chloride
1.0 mMMgCl2Magnesium Chloride
Sugar embeddingMaterial: buffer
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: MOLYBDENUM / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 24 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.86758 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.813 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 beta2) / Details: Half-map generation is Gold-standard / Number images used: 114110
CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: NONE
Segment selectionNumber selected: 197442
Startup modelType of model: OTHER / Details: CryoEM map of FliC flagellar filament
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0 beta-2)
FSC plot (resolution estimation)

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