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- PDB-1ucu: R-type straight flagellar filament made of full-length flagellin -

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Basic information

Entry
Database: PDB / ID: 1ucu
TitleR-type straight flagellar filament made of full-length flagellin
Componentsphase 1 Flagellin
KeywordsSTRUCTURAL PROTEIN / FLAGELLIN / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION
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
AuthorsYonekura, K. / Maki-Yonekura, S. / Namba, K.
Citation
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.
#1: Journal: NATURE / Year: 2001
Title: Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling
Authors: Samatey, F.A. / Imada, K. / Nagashima, S. / Vonderviszt, F. / Kumasaka, T. / Yamamoto, M. / Namba, K.
History
DepositionApr 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Experimental preparation / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_image_scans / em_single_particle_entity / em_vitrification / pdbx_initial_refinement_model / struct_keywords
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_keywords.pdbx_keywords
Remark 244 OTHER_DETAILS: REPEAT DISTANCE (ANGSTROMS) : 1698.8 BASIC HELIX INDEX (N10, L10) : ( 11, 4) (N01, ... OTHER_DETAILS: REPEAT DISTANCE (ANGSTROMS) : 1698.8 BASIC HELIX INDEX (N10, L10) : ( 11, 4) (N01, L01) : ( -5, 31) SELECTION RULE : L = 66 N + 361 M MAXIMUM BESSEL ORDER : 170 NUMBER OF LAYER-LINES : 298 NUMBER OF FILAMENT IMAGES : 102 NUMBER OF MOLECULAR IMAGES : 41,469 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.000 ALONG THE MERIDIAN EFFECTIVE RESOLUTION (ANGSTROMS) : 5.000 ALONG THE EQUATOR
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

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Assembly

Deposited unit
A: phase 1 Flagellin


Theoretical massNumber of molelcules
Total (without water)51,5511
Polymers51,5511
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 phase 1 Flagellin


Mass: 51551.203 Da / Num. of mol.: 1 / Mutation: A449V / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Strain: SJW 1665 / References: UniProt: P06179

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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: R-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)
Crystal grow
*PLUS
Method: unknown

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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: 47600 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 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

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Processing

Software
NameClassification
FEX-PLORrefinement
FX-PLORrefinement
EM softwareName: X-PLOR / Category: model fitting
CTF correctionDetails: BOTH AMPLITUDE AND PHASE
3D reconstructionMethod: HELICAL RECONSTRUCTION / Resolution: 4 Å / Num. of particles: 102 / Nominal pixel size: 1 Å / Actual pixel size: 1.05 Å
Magnification calibration: R-TYPE STRAIGHT FLAGELLAR FILAMENT
Details: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin ...Details: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin was built by tracing missing terminal chains. The model was refined using both positional and simulated annealing refinements, by a molecular dynamics refinement program, FEX-PLOR, which we developed based on FX-PLOR for EM image analysis of the helical assembly. The amplitude-weighted phase-residual was implemented as an effective potential energy. The layer-line amplitude distributions of the EM data were then scaled to the structure factors calculated from the model based on their radial amplitude profiles obtained by averaging the amplitudes within each resolution shell. The density map was calculated again, and model building and refinement were iterated.
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: amplitude-weighted phase residual
Details: REFINEMENT PROTOCOL--POSITIONAL AND SIMULATED ANNEALING
Atomic model buildingPDB-ID: 1IO1
Accession code: 1IO1 / Source name: PDB / Type: experimental model
RefinementResolution: 4→30 Å / Rfactor Rwork: 0.3
Refinement stepCycle: LAST / Resolution: 4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 0 0 3617

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