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- PDB-6k9q: Structure of the native supercoiled hook as a universal joint -

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Basic information

Entry
Database: PDB / ID: 6k9q
TitleStructure of the native supercoiled hook as a universal joint
ComponentsFlagellar hook protein FlgE
KeywordsMOTOR PROTEIN / Flagella motor / Hook / Native structure / Supercoiled / FlgE
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum-dependent cell 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 / Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKato, T. / Miyata, T. / Makino, F. / Horvath, P. / Namba, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25000013 Japan
Japan Society for the Promotion of Science (JSPS)18K06155 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the native supercoiled flagellar hook as a universal joint.
Authors: Takayuki Kato / Fumiaki Makino / Tomoko Miyata / Péter Horváth / Keiichi Namba /
Abstract: The Bacterial flagellar hook is a short supercoiled tubular structure made from a helical assembly of the hook protein FlgE. The hook acts as a universal joint that connects the flagellar basal body ...The Bacterial flagellar hook is a short supercoiled tubular structure made from a helical assembly of the hook protein FlgE. The hook acts as a universal joint that connects the flagellar basal body and filament, and smoothly transmits torque generated by the rotary motor to the helical filament propeller. In peritrichously flagellated bacteria, the hook allows the filaments to form a bundle behind the cell for swimming, and for the bundle to fall apart for tumbling. Here we report a native supercoiled hook structure at 3.6 Å resolution by cryoEM single particle image analysis of the polyhook. The atomic model built into the three-dimensional (3D) density map reveals the changes in subunit conformation and intersubunit interactions that occur upon compression and extension of the 11 protofilaments during their smoke ring-like rotation. These observations reveal how the hook functions as a dynamic molecular universal joint with high bending flexibility and twisting rigidity.
History
DepositionJun 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

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  • Simplified surface model + fitted atomic model
  • EMDB-9952
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar hook protein FlgE
B: Flagellar hook protein FlgE
C: Flagellar hook protein FlgE
D: Flagellar hook protein FlgE
E: Flagellar hook protein FlgE
F: Flagellar hook protein FlgE
G: Flagellar hook protein FlgE
H: Flagellar hook protein FlgE
I: Flagellar hook protein FlgE
J: Flagellar hook protein FlgE
K: Flagellar hook protein FlgE
L: Flagellar hook protein FlgE
M: Flagellar hook protein FlgE
N: Flagellar hook protein FlgE
O: Flagellar hook protein FlgE
P: Flagellar hook protein FlgE
Q: Flagellar hook protein FlgE
R: Flagellar hook protein FlgE
S: Flagellar hook protein FlgE
T: Flagellar hook protein FlgE
U: Flagellar hook protein FlgE
V: Flagellar hook protein FlgE
W: Flagellar hook protein FlgE
X: Flagellar hook protein FlgE
Y: Flagellar hook protein FlgE
Z: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)1,094,65126
Polymers1,094,65126
Non-polymers00
Water0
1


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

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Components

#1: Protein ...
Flagellar hook protein FlgE


Mass: 42101.957 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: A0A0J1A5C1, UniProt: P0A1J1*PLUS

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Native supercoiled hook / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 42979 kDa/nm / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisC4H11NO31
2100 mMNaClSodium chlorideNaClSodium chloride1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 291 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Cs: 1.4 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 100.5 K / Temperature (min): 99.7 K
Image recordingAverage exposure time: 10 sec. / Electron dose: 0.87 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1702
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 2-50

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Processing

EM software
IDNameVersionCategory
4Gctf1.06CTF correction
7UCSF Chimera1.11model fitting
8Coot0.8.9model fitting
10cryoSPARC2initial Euler assignment
11cryoSPARC2final Euler assignment
12cryoSPARC2classification
13cryoSPARC23D reconstruction
14PHENIX1.13model refinement
15Coot0.8.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 418814
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157334 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-IDPdb chain residue range
13A69

3a69

3A6911-402
25JXL

5jxl

5JXL228-46
35JXL

5jxl

5JXL265-92

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