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- PDB-6jy0: CryoEM structure of S.typhimurium R-type straight flagellar filam... -

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Basic information

Entry
Database: PDB / ID: 6jy0
TitleCryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V)
ComponentsFlagellin
KeywordsPROTEIN FIBRIL / FljB / Helical reconstruction / Salmonella / Flagellar motor
Function / homology
Function and homology information


bacterial-type flagellum filament / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
Flagellin D3 / Flagellin D3 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsYamaguchi, T. / Toma, S. / Terahara, N. / Miyata, T. / Minamino, T. / Ashikara, M. / Namba, K. / Kato, T.
Funding support Japan, 1items
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
W: Flagellin


Theoretical massNumber of molelcules
Total (without water)1,157,38622
Polymers1,157,38622
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellin /


Mass: 52608.449 Da / Num. of mol.: 22 / Mutation: A461V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fljB, C2253_13415, CET98_21075, D7F20_13880, D7H43_12410, DJ388_21755
Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: Q549S3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: FljB / Type: COMPLEX / Details: R-type straight flagellar filament (A461V) / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SJW590
Source (recombinant)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris (hydroxymethyl) amino methaneTris-HClTris1
2150 mMSodium chlorideNaClSodium chloride1
31 mMMagnesium ChlorideMgCl21
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
EM embeddingMaterial: buffer
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 72273 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 210 nm / Calibrated defocus max: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 10.3 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 2319
Image scansMovie frames/image: 7 / Used frames/image: 1-6

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2RELION3image acquisitionbeta-2
4Gctf1.06CTF correction
9RELION3initial Euler assignmentbeta-2
10RELION3.0 beta-2final Euler assignment
11RELION3.0 beta-2classification
12RELION3.0 beta23D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 65.813 ° / Axial rise/subunit: 4.86758 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 197442
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114110 / Details: Half-map generation is Gold-standard / Symmetry type: HELICAL

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