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- PDB-5jxl: Cryo-EM structure of the flagellar hook of Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 5jxl
TitleCryo-EM structure of the flagellar hook of Campylobacter jejuni
Componentsflagellar hook protein FlgE
KeywordsMOTOR PROTEIN / Campylobacter jejuni / helical assembly of FlgE / flagellar hook
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility
Similarity search - Function
Flagellar hook FlgE / Flagellar hook protein FlgE, D3 domain / Flagellin hook IN motif / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain ...Flagellar hook FlgE / Flagellar hook protein FlgE, D3 domain / Flagellin hook IN motif / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni 81116 (Campylobacter)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMatsunami, H. / Wolf, M. / Samatey, F.A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Okinawa Institute of Science and Technology Graduate University Japan
CitationJournal: Nat Commun / Year: 2016
Title: Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions.
Authors: Hideyuki Matsunami / Clive S Barker / Young-Ho Yoon / Matthias Wolf / Fadel A Samatey /
Abstract: The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by ...The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by cryo-electron microscopy at a resolution of 3.5 Å. On the basis of this structure, we show that the hook is stabilized by intricate inter-molecular interactions between FlgE molecules. Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off. This structure reveals details of the quaternary organization of the hook that consists of 11 protofilaments. Previous study of the flagellar filament of Campylobacter by electron microscopy showed its quaternary structure made of seven protofilaments. Therefore, this study puts in evidence the difference between the quaternary structures of a bacterial filament and its hook.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Other
Revision 1.2Jul 25, 2018Group: Data collection / Category: em_software / Item: _em_software.details / _em_software.name
Revision 1.3Dec 11, 2019Group: Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.4Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Simplified surface model + fitted atomic model
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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)90,4501
Polymers90,4501
Non-polymers00
Water00
1
A: flagellar hook protein FlgE
x 11


Theoretical massNumber of molelcules
Total (without water)994,94711
Polymers994,94711
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: 4.185 Å / Rotation per n subunits: 64.34 °)

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Components

#1: Protein flagellar hook protein FlgE


Mass: 90449.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Campylobacter jejuni subsp. jejuni 81116 (Campylobacter)
Strain: 81116 / References: UniProt: A0A1L1QK18*PLUS

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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: Campylobacter Hook / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Buffer solutionpH: 8 / Details: EDTA, Triton X-100
Buffer componentConc.: 10 mM / Name: Tris Hydrochloride / Formula: Tris-HCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 280 K
Details: blotting from both side, Whatman #40 filter paper, 25 seconds blot time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: parallel illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 79000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 63 K
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 2.4 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 504
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 18 / Used frames/image: 1-5

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Processing

EM software
IDNameVersionCategoryDetails
1e2helixboxer.py2.12particle selection
2Leginon3.1image acquisition
4ctffind33.5CTF correction
5CTFTILT1.7CTF correction
8Coot0.8.3model fitting
9O14model fitting
11segclassreconstruct0.83initial Euler assignmentSPRING package
12segrefine3d0.83final Euler assignmentSPRING package
13segmentclass0.83classificationSPRING package
14segrefine3d0.833D reconstructionSPRING package
15PHENIX1.9-1692model refinementphenix_real_space_refine
Image processingDetails: first 5 images were aligned for drift correction and summed. Summed images were normalizaed.
CTF correctionDetails: SPRING v0.83 / Type: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 64.34 ° / Axial rise/subunit: 4.185 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 70477
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49884 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingB value: 120 / Protocol: BACKBONE TRACE / Space: REAL / Target criteria: CC / Details: side chains included, default parameters
Atomic model buildingPDB-ID: 5AZ4

5az4


Pdb chain-ID: A / Accession code: 5AZ4 / Source name: PDB / Type: experimental model

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