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- PDB-3a69: Atomic model of the bacterial flagellar hook based on docking an ... -

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Basic information

Entry
Database: PDB / ID: 3a69
TitleAtomic model of the bacterial flagellar hook based on docking an X-ray derived structure and terminal two alpha-helices into an 7.1 angstrom resolution cryoEM map
ComponentsFlagellar hook protein flgE
KeywordsMOTOR PROTEIN / the bacterial flagellar motor / universal joint / Bacterial flagellum
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsFujii, T. / Kato, T. / Namba, K.
CitationJournal: Structure / Year: 2009
Title: Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function.
Authors: Takashi Fujii / Takayuki Kato / Keiichi Namba /
Abstract: The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to ...The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to work as a universal joint. A partial atomic model of the hook revealed a sliding intersubunit domain interaction along the protofilament to produce bending flexibility. However, it remained unclear how the tightly packed inner core domains can still permit axial extension and compression. We report advances in cryoEM image analysis for high-resolution, high-throughput structural analysis and a density map of the hook that reveals most of the secondary structures, including the terminal alpha helices forming a coiled coil. The orientations and axial packing interactions of these two alpha helices are distinctly different from those of the filament, allowing them to have a room for axial compression and extension for bending flexibility without impairing the mechanical stability of the hook.
History
DepositionAug 26, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Other
Category: cell / database_2 ...cell / database_2 / em_image_scans / em_single_particle_entity
Item: _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-1647
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Flagellar hook protein flgE


Theoretical massNumber of molelcules
Total (without water)42,1021
Polymers42,1021
Non-polymers00
Water0
1
A: Flagellar hook protein flgE
x 11


Theoretical massNumber of molelcules
Total (without water)463,12211
Polymers463,12211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation10
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 11 / Rise per n subunits: 4.123 Å / Rotation per n subunits: 64.786 °)

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Components

#1: Protein Flagellar hook protein flgE


Mass: 42101.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SJW880 / References: UniProt: P0A1J1

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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: bacterial flagellar hook / Type: COMPLEX
Buffer solutionName: 20mM Tris-HCl, 100mM NaCl / pH: 7 / Details: 20mM Tris-HCl, 100mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: HELIUM / Humidity: 90 %

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Feb 20, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 89285 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 1.6 mm
Specimen holderSpecimen holder model: JEOL
Specimen holder type: Top entry liquid helium-cooled cryo specimen holder
Temperature: 50 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
EM imaging opticsEnergyfilter upper: 10 eV / Energyfilter lower: 0 eV
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

CTF correctionDetails: each images
3D reconstructionMethod: IHRSR / Resolution: 7.1 Å / Actual pixel size: 1.68 Å / Magnification calibration: TMV images
Details: a modified version of SPIDER program was used for the reconstruction
Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 0 0 2573

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