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- PDB-5wrh: FlgG structure based on the CryoEM map of the bacterial flagellar... -

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Basic information

Entry
Database: PDB / ID: 5wrh
TitleFlgG structure based on the CryoEM map of the bacterial flagellar polyrod
ComponentsFlagellar basal-body rod protein FlgG
KeywordsMOTOR PROTEIN / the bacterial flagellar motor
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar basal-body rod FlgG / 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 basal-body rod protein FlgG
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsFujii, T. / Namba, K.
CitationJournal: Nat Commun / Year: 2017
Title: Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook.
Authors: Takashi Fujii / Takayuki Kato / Koichi D Hiraoka / Tomoko Miyata / Tohru Minamino / Fabienne F V Chevance / Kelly T Hughes / Keiichi Namba /
Abstract: The bacterial flagellum is a motile organelle driven by a rotary motor, and its axial portions function as a drive shaft (rod), a universal joint (hook) and a helical propeller (filament). The rod ...The bacterial flagellum is a motile organelle driven by a rotary motor, and its axial portions function as a drive shaft (rod), a universal joint (hook) and a helical propeller (filament). The rod and hook are directly connected to each other, with their subunit proteins FlgG and FlgE having 39% sequence identity, but show distinct mechanical properties; the rod is straight and rigid as a drive shaft whereas the hook is flexible in bending as a universal joint. Here we report the structure of the rod and comparison with that of the hook. While these two structures have the same helical symmetry and repeat distance and nearly identical folds of corresponding domains, the domain orientations differ by ∼7°, resulting in tight and loose axial subunit packing in the rod and hook, respectively, conferring the rigidity on the rod and flexibility on the hook. This provides a good example of versatile use of a protein structure in biological organisms.
History
DepositionDec 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Flagellar basal-body rod protein FlgG


Theoretical massNumber of molelcules
Total (without water)27,7851
Polymers27,7851
Non-polymers00
Water0
1
A: Flagellar basal-body rod protein FlgG
x 22


Theoretical massNumber of molelcules
Total (without water)611,26622
Polymers611,26622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation22
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 22 / Rise per n subunits: 4.13 Å / Rotation per n subunits: 64.723 °)

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Components

#1: Protein Flagellar basal-body rod protein FlgG / Distal rod protein


Mass: 27784.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P0A1J3

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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: the bacterial flagellar polyrod / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 64.75 ° / Axial rise/subunit: 4.13 Å / Axial symmetry: C1
3D reconstructionResolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 10645 / Symmetry type: HELICAL

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