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- PDB-6jzt: Structure of the bacterial flagellar hook from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 6jzt
TitleStructure of the bacterial flagellar hook from Salmonella typhimurium
ComponentsFlagellar hook protein FlgE
KeywordsMOTOR PROTEIN / Bacterial flagellum / hook protein / STRUCTURAL PROTEIN
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 / helical reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsSaijo-Hamano, Y. / Matsunami, H. / Namba, K. / Imada, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP24570132 Japan
Japan Society for the Promotion of ScienceJP25000013 Japan
Japan Society for the Promotion of ScienceJP21227006 Japan
Japan Society for the Promotion of ScienceJP15H02386 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP23115008 Japan
CitationJournal: Biomolecules / Year: 2019
Title: Architecture of the Bacterial Flagellar Distal Rod and Hook of .
Authors: Yumiko Saijo-Hamano / Hideyuki Matsunami / Keiichi Namba / Katsumi Imada /
Abstract: The bacterial flagellum is a large molecular complex composed of thousands of protein subunits for motility. The filamentous part of the flagellum, which is called the axial structure, consists of ...The bacterial flagellum is a large molecular complex composed of thousands of protein subunits for motility. The filamentous part of the flagellum, which is called the axial structure, consists of the filament, the hook, and the rods, with other minor components-the cap protein and the hook associated proteins. They share a common basic architecture of subunit arrangement, but each part shows quite distinct mechanical properties to achieve its specific function. The distal rod and the hook are helical assemblies of a single protein, FlgG and FlgE, respectively. They show a significant sequence similarity but have distinct mechanical characteristics. The rod is a rigid, straight cylinder, whereas the hook is a curved tube with high bending flexibility. Here, we report a structural model of the rod constructed by using the crystal structure of a core fragment of FlgG with a density map obtained previously by electron cryomicroscopy. Our structural model suggests that a segment called L-stretch plays a key role in achieving the distinct mechanical properties of the rod using a structurally similar component protein to that of the hook.
History
DepositionMay 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
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


Theoretical massNumber of molelcules
Total (without water)929,12922
Polymers929,12922
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: 42233.152 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Variant: SJW880 / 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: helical reconstruction

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Sample preparation

ComponentName: The flagellar hook / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SJW880
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

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 64.78 ° / Axial rise/subunit: 4.12 Å / Axial symmetry: C1
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 200 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00366044
ELECTRON MICROSCOPYf_angle_d0.59489980
ELECTRON MICROSCOPYf_dihedral_angle_d9.86539072
ELECTRON MICROSCOPYf_chiral_restr0.04210560
ELECTRON MICROSCOPYf_plane_restr0.00412078

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