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- PDB-3a5x: L-type straight flagellar filament made of full-length flagellin -

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Basic information

Entry
Database: PDB / ID: 3a5x
TitleL-type straight flagellar filament made of full-length flagellin
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / MOTOR PROTEIN / FLAGELLIN / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION / Bacterial flagellum / Secreted
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #190 / f41 fragment of flagellin, middle domain / f41 fragment of flagellin, middle domain / f41 fragment of flagellin, C-terminal domain / f41 fragment of flagellin, C-terminal domain / : / Flagellin, barrel domain / Flagellin D3 / Flagellin D3 domain / f41 fragment of flagellin, N-terminal domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #190 / f41 fragment of flagellin, middle domain / f41 fragment of flagellin, middle domain / f41 fragment of flagellin, C-terminal domain / f41 fragment of flagellin, C-terminal domain / : / Flagellin, barrel domain / Flagellin D3 / Flagellin D3 domain / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Beta Complex / Helix non-globular / Special / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsMaki-Yonekura, S. / Yonekura, K. / Namba, K.
Citation
Journal: Nat Struct Mol Biol / Year: 2010
Title: Conformational change of flagellin for polymorphic supercoiling of the flagellar filament.
Authors: Saori Maki-Yonekura / Koji Yonekura / Keiichi Namba /
Abstract: The bacterial flagellar filament is a helical propeller rotated by the flagellar motor for bacterial locomotion. The filament is a supercoiled assembly of a single protein, flagellin, and is formed ...The bacterial flagellar filament is a helical propeller rotated by the flagellar motor for bacterial locomotion. The filament is a supercoiled assembly of a single protein, flagellin, and is formed by 11 protofilaments. For bacterial taxis, the reversal of motor rotation switches the supercoil between left- and right-handed, both of which arise from combinations of two distinct conformations and packing interactions of the L-type and R-type protofilaments. Here we report an atomic model of the L-type straight filament by electron cryomicroscopy and helical image analysis. Comparison with the R-type structure shows interesting features: an orientation change of the outer core domains (D1) against the inner core domains (D0) showing almost invariant orientation and packing, a conformational switching within domain D1, and the conformational flexibility of domains D0 and D1 with their spoke-like connection for tight molecular packing.
#1: Journal: Nature / Year: 2001
Title: Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling.
Authors: F A Samatey / K Imada / S Nagashima / F Vonderviszt / T Kumasaka / M Yamamoto / K Namba /
Abstract: The bacterial flagellar filament is a helical propeller constructed from 11 protofilaments of a single protein, flagellin. The filament switches between left- and right-handed supercoiled forms when ...The bacterial flagellar filament is a helical propeller constructed from 11 protofilaments of a single protein, flagellin. The filament switches between left- and right-handed supercoiled forms when bacteria switch their swimming mode between running and tumbling. Supercoiling is produced by two different packing interactions of flagellin called L and R. In switching from L to R, the intersubunit distance ( approximately 52 A) along the protofilament decreases by 0.8 A. Changes in the number of L and R protofilaments govern supercoiling of the filament. Here we report the 2.0 A resolution crystal structure of a Salmonella flagellin fragment of relative molecular mass 41,300. The crystal contains pairs of antiparallel straight protofilaments with the R-type repeat. By simulated extension of the protofilament model, we have identified possible switch regions responsible for the bi-stable mechanical switch that generates the 0.8 A difference in repeat distance.
#2: Journal: Nature / Year: 2003
Title: Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy.
Authors: Koji Yonekura / Saori Maki-Yonekura / Keiichi Namba /
Abstract: The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in ...The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in two distinct conformations, L- and R-type, for supercoiling. The X-ray crystal structure of a flagellin fragment lacking about 100 terminal residues revealed the protofilament structure, but the full filament structure is still essential for understanding the mechanism of supercoiling and polymerization. Here we report a complete atomic model of the R-type filament by electron cryomicroscopy. A density map obtained from image data up to 4 A resolution shows the feature of alpha-helical backbone and some large side chains. The atomic model built on the map reveals intricate molecular packing and an alpha-helical coiled coil formed by the terminal chains in the inner core of the filament, with its intersubunit hydrophobic interactions having an important role in stabilizing the filament.
History
DepositionAug 13, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Database references
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Data collection / Database references
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Assembly

Deposited unit
A: Flagellin


Theoretical massNumber of molelcules
Total (without water)51,5371
Polymers51,5371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Flagellin / / L-type flagellin / Phase 1-I flagellin


Mass: 51537.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Strain: SJW1660 / References: UniProt: P06179
Sequence detailsA NATURAL MUTATION AT THIS POSITION

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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: L-TYPE STRAIGHT FLAGELLAR FILAMENT / Type: COMPLEX
Buffer solutionName: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL / pH: 7.8
Details: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: QUANTIFOIL R1.2/1.3 (25 NM THICK)
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 2220 nm / Nominal defocus min: 1080 nm / Cs: 1.6 mm
Specimen holderTemperature: 4 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: FEX-PLOR / Classification: refinement
EM software
IDNameCategory
1X-PLORmodel fitting
2Custom3D reconstruction
CTF correctionDetails: Both amplitude and phase
3D reconstructionMethod: Helical reconstruction / Resolution: 4 Å / Nominal pixel size: 1 Å / Actual pixel size: 1 Å
Magnification calibration: L-TYPE STRAIGHT flagellar filament
Details: The layer-line spacing of the L-type straight flagellar filament is more than twice longer than that of the R-type, and frozen-hydrated L-type filaments tended to be more curved. Hence, ...Details: The layer-line spacing of the L-type straight flagellar filament is more than twice longer than that of the R-type, and frozen-hydrated L-type filaments tended to be more curved. Hence, straightening of images using bi-cubic spline was carried out at the first stage. The three-dimensional map was calculated by helical image reconstruction. An initial map produced from 70 filament images, corresponding to 51,272 molecular images, showed relatively poor connections of the ND0 helix and the NS loop. Hence, images showing an inter-particle phase residual against the initial average larger than 40 were excluded from the data set to be averaged. As a result, a three-dimensional map of a better quality was obtained. The number of filament images used for the final image reconstruction was 47, and the total number of molecular images was 36,842, which is consistent with an estimated number of molecular images required to achieve this resolution range.
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: AMPLITUDE-WEIGHTED PHASE RESIDUAL
Details: REFINEMENT PROTOCOL--POSITIONAL AND SIMULATED ANNEALING
RefinementHighest resolution: 4 Å
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 0 0 3616

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