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- PDB-6k3i: Salmonella hook in curved state - 66 subunit models -

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Basic information

Entry
Database: PDB / ID: 6k3i
TitleSalmonella hook in curved state - 66 subunit models
ComponentsFlagellar hook protein FlgE
KeywordsMOTOR PROTEIN / bacterial / hook / flexible joint / flagella
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 typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsShibata, S. / Matsunami, H. / Wolf, M. / Aizawa, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of Science17K17085 Japan
Japan Society for the Promotion of Science19K10083 Japan
Japan Society for the Promotion of Science17K07318 Japan
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Torque transmission mechanism of the curved bacterial flagellar hook revealed by cryo-EM.
Authors: Satoshi Shibata / Hideyuki Matsunami / Shin-Ichi Aizawa / Matthias Wolf /
Abstract: Bacterial locomotion by rotating flagella is achieved through the hook, which transmits torque from the motor to the filament. The hook is a tubular structure composed of a single type of protein, ...Bacterial locomotion by rotating flagella is achieved through the hook, which transmits torque from the motor to the filament. The hook is a tubular structure composed of a single type of protein, yet it adopts a curved shape. To perform its function, it must be simultaneously flexible and torsionally rigid. The molecular mechanism by which chemically identical subunits form such a dynamic structure is unknown. Here, we show the complete structure of the hook from Salmonella enterica in its supercoiled 'curved' state, at 2.9 Å resolution. Subunits in the curved hook are grouped into 11 distinctive conformations, each shared along 11 protofilaments. The domains of the elongated hook subunit behave as rigid bodies connected by two hinge regions. The reconstituted model demonstrates how identical subunits can dynamically change conformation by physical interactions while bending. These multiple subunit states contradict the two-state model, which is a key feature of flagellar polymorphism.
History
DepositionMay 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 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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Structure viewerMolecule:
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Assembly

Deposited unit
AA: Flagellar hook protein FlgE
AB: Flagellar hook protein FlgE
AC: Flagellar hook protein FlgE
AD: Flagellar hook protein FlgE
AE: Flagellar hook protein FlgE
AF: Flagellar hook protein FlgE
AG: Flagellar hook protein FlgE
AH: Flagellar hook protein FlgE
AI: Flagellar hook protein FlgE
AJ: Flagellar hook protein FlgE
AK: Flagellar hook protein FlgE
BA: Flagellar hook protein FlgE
BB: Flagellar hook protein FlgE
BC: Flagellar hook protein FlgE
BD: Flagellar hook protein FlgE
BE: Flagellar hook protein FlgE
BF: Flagellar hook protein FlgE
BG: Flagellar hook protein FlgE
BH: Flagellar hook protein FlgE
BI: Flagellar hook protein FlgE
BJ: Flagellar hook protein FlgE
BK: Flagellar hook protein FlgE
CA: Flagellar hook protein FlgE
CB: Flagellar hook protein FlgE
CC: Flagellar hook protein FlgE
CD: Flagellar hook protein FlgE
CE: Flagellar hook protein FlgE
CF: Flagellar hook protein FlgE
CG: Flagellar hook protein FlgE
CH: Flagellar hook protein FlgE
CI: Flagellar hook protein FlgE
CJ: Flagellar hook protein FlgE
CK: Flagellar hook protein FlgE
DA: Flagellar hook protein FlgE
DB: Flagellar hook protein FlgE
DC: Flagellar hook protein FlgE
DD: Flagellar hook protein FlgE
DE: Flagellar hook protein FlgE
DF: Flagellar hook protein FlgE
DG: Flagellar hook protein FlgE
DH: Flagellar hook protein FlgE
DI: Flagellar hook protein FlgE
DJ: Flagellar hook protein FlgE
DK: Flagellar hook protein FlgE
EA: Flagellar hook protein FlgE
EB: Flagellar hook protein FlgE
EC: Flagellar hook protein FlgE
ED: Flagellar hook protein FlgE
EE: Flagellar hook protein FlgE
EF: Flagellar hook protein FlgE
EG: Flagellar hook protein FlgE
EH: Flagellar hook protein FlgE
EI: Flagellar hook protein FlgE
EJ: Flagellar hook protein FlgE
EK: Flagellar hook protein FlgE
FA: Flagellar hook protein FlgE
FB: Flagellar hook protein FlgE
FC: Flagellar hook protein FlgE
FD: Flagellar hook protein FlgE
FE: Flagellar hook protein FlgE
FF: Flagellar hook protein FlgE
FG: Flagellar hook protein FlgE
FH: Flagellar hook protein FlgE
FI: Flagellar hook protein FlgE
FJ: Flagellar hook protein FlgE
FK: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)2,778,72966
Polymers2,778,72966
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.: 66 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P0A1J1

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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: Bacterial flagellar polyhook / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.8 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 3.5
Buffer componentConc.: 50 mM / Name: Glycine / Formula: C2H5NO2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K / Details: 3 second blot, 4.0uL

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: nanoprobe, parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Calibrated magnification: 107914 X / Nominal defocus max: 5130 nm / Nominal defocus min: 430 nm / Calibrated defocus min: 430 nm / Calibrated defocus max: 5130 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 77 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 89 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2655
Details: frame alignment and dose weighting using motioncor2
Image scansSampling size: 15 µm / Width: 4000 / Height: 4000

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Processing

EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.8.9model fitting
9PHENIX1.14-3260model refinementphenix.real_space_refine
10cisTEM1.0.1-betainitial Euler assignment
11cisTEM1.0.1-betafinal Euler assignment
12cisTEM1.0.1-betaclassification
13cisTEM1.0.1-beta3D reconstruction
Image processingDetails: frame alignment and integration with motioncor2 incl. dose weighting
CTF correctionDetails: deconvolution in cisTEM / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 998061
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 234536 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: CC
Atomic model buildingPDB-ID: 1WLG

1wlg


Pdb chain-ID: A / Accession code: 1WLG / Pdb chain residue range: 70-359 / Source name: PDB / Type: experimental model

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