- PDB-6k9q: Structure of the native supercoiled hook as a universal joint -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6k9q
Title
Structure of the native supercoiled hook as a universal joint
Components
Flagellar hook protein FlgE
Keywords
MOTOR 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 Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / 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
Japan Agency for Medical Research and Development (AMED)
JP19am0101117
Japan
Japan Agency for Medical Research and Development (AMED)
JP17pc0101020
Japan
Citation
Journal: 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.
#262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (12)
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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
Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 291 K
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Electron microscopy imaging
Microscopy
Model: JEOL CRYO ARM 200
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lens
Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Cs: 1.4 mm / Alignment procedure: COMA FREE
Specimen holder
Cryogen: NITROGEN / Temperature (max): 100.5 K / Temperature (min): 99.7 K
Image recording
Average 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
Width: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 2-50
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Processing
EM software
ID
Name
Version
Category
4
Gctf
1.06
CTFcorrection
7
UCSF Chimera
1.11
modelfitting
8
Coot
0.8.9
modelfitting
10
cryoSPARC
2
initialEulerassignment
11
cryoSPARC
2
finalEulerassignment
12
cryoSPARC
2
classification
13
cryoSPARC
2
3Dreconstruction
14
PHENIX
1.13
modelrefinement
15
Coot
0.8.9
modelrefinement
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
Num. of particles selected: 418814
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 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 building
Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building
3D fitting-ID: 1 / Pdb chain-ID: A / Source name: PDB / Type: experimental model
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