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- PDB-2bgz: ATOMIC MODEL OF THE BACTERIAL FLAGELLAR BASED ON DOCKING AN X-RAY... -

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Entry
Database: PDB / ID: 2bgz
TitleATOMIC MODEL OF THE BACTERIAL FLAGELLAR BASED ON DOCKING AN X-RAY DERIVED HOOK STRUCTURE INTO AN EM MAP.
ComponentsFLAGELLAR HOOK PROTEIN FLGE
KeywordsMOTOR PROTEIN / BACTERIAL MOTIILITY / BACTERIAL FLAGELLAR HOOK / FLAGELLUM
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 / Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodELECTRON MICROSCOPY / electron crystallography / cryo EM / Resolution: 9 Å
AuthorsShaikh, T.R. / Thomas, D.R. / Chen, J.Z. / Samatey, F.A. / Matsunami, H. / Imada, K. / Namba, K. / Derosier, D.J.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2005
Title: A partial atomic structure for the flagellar hook of Salmonella typhimurium.
Authors: Tanvir R Shaikh / Dennis R Thomas / James Z Chen / Fadel A Samatey / Hideyuki Matsunami / Katsumi Imada / Keiichi Namba / David J Derosier /
Abstract: The axial proteins of the bacterial flagellum function as a drive shaft, universal joint, and propeller driven by the flagellar rotary motor; they also form the putative protein export channel. The N- ...The axial proteins of the bacterial flagellum function as a drive shaft, universal joint, and propeller driven by the flagellar rotary motor; they also form the putative protein export channel. The N- and C-terminal sequences of the eight axial proteins were predicted to form interlocking alpha-domains generating an axial tube. We report on an approximately 1-nm resolution map of the hook from Salmonella typhimurium, which reveals such a tube made from interdigitated, 1-nm rod-like densities similar to those seen in maps of the filament. Atomic models for the two outer domains of the hook subunit were docked into the corresponding outermost features of the map. The N and C termini of the hook subunit fragment are positioned next to each other and face toward the axis of the hook. The placement of these termini would permit the residues missing in the fragment to form the rod-like features that form the core domain of the hook. We also fit the hook atomic model to an approximately 2-nm resolution map of the hook from Caulobacter crescentus. The hook protein sequence from C. crescentus is largely homologous to that of S. typhimurium except for a large insertion (20 kDa). According to difference maps and our fitting, this insertion is found on the outer surface of the hook, consistent with our modeling of the hook.
#1: Journal: Nature / Year: 2004
Title: Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism.
Authors: Fadel A Samatey / Hideyuki Matsunami / Katsumi Imada / Shigehiro Nagashima / Tanvir R Shaikh / Dennis R Thomas / James Z Chen / David J Derosier / Akio Kitao / Keiichi Namba /
Abstract: The bacterial flagellum is a motile organelle, and the flagellar hook is a short, highly curved tubular structure that connects the flagellar motor to the long filament acting as a helical propeller. ...The bacterial flagellum is a motile organelle, and the flagellar hook is a short, highly curved tubular structure that connects the flagellar motor to the long filament acting as a helical propeller. The hook is made of about 120 copies of a single protein, FlgE, and its function as a nano-sized universal joint is essential for dynamic and efficient bacterial motility and taxis. It transmits the motor torque to the helical propeller over a wide range of its orientation for swimming and tumbling. Here we report a partial atomic model of the hook obtained by X-ray crystallography of FlgE31, a major proteolytic fragment of FlgE lacking unfolded terminal regions, and by electron cryomicroscopy and three-dimensional helical image reconstruction of the hook. The model reveals the intricate molecular interactions and a plausible switching mechanism for the hook to be flexible in bending but rigid against twisting for its universal joint function.
History
DepositionJan 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Assembly

Deposited unit
A: FLAGELLAR HOOK PROTEIN FLGE


Theoretical massNumber of molelcules
Total (without water)31,3351
Polymers31,3351
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein FLAGELLAR HOOK PROTEIN FLGE


Mass: 31335.084 Da / Num. of mol.: 1 / Fragment: FLGE31, RESIDUES 71-369
Source method: isolated from a genetically manipulated source
Details: FIT OF CRYSTAL STRUCTURE PDB ID 1WLG TO AN EM AMAP OF S. TYPHIMURIUM POLYHOOK
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P16322, UniProt: P0A1J1*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: POLYHOOK / Type: COMPLEX
Buffer solutionName: 10 MM TRIS/HCL,5MM EDTA,0. 1%V/V TRITON X-100 / pH: 8 / Details: 10 MM TRIS/HCL,5MM EDTA,0. 1%V/V TRITON X-100
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: SAMPLES PREPARED AT 4 DEG C PLUNGED INTO LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG
Details: DATA FROM 262 INDIVIDUAL SEGMENTS OF HOOK IN FINAL MAP.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 66000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1300 nm / Cs: 2 mm
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1RSRefmodel fitting
2Brandeis Helical Package3D reconstruction
3D reconstructionResolution: 9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Details: HELICAL SYMMETRY OPERATORS CAN BE CALCULATED USING RISE PER SUBUNIT 4.226475A ROTATION PER SUBUNIT 23.48758 DEG. DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH 12A, RESOLUTION RANGE LOW ...Details: HELICAL SYMMETRY OPERATORS CAN BE CALCULATED USING RISE PER SUBUNIT 4.226475A ROTATION PER SUBUNIT 23.48758 DEG. DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH 12A, RESOLUTION RANGE LOW 200A, DATA CUTOFF (SIGMA(F)) 1, COMPLETENESS FOR RANGE 100(%) NUMBER OF REFLECTIONS 84. PROTEIN ATOMS 2156
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Details: METHOD--RECIPROCAL SPACE FITTING IN URO
RefinementHighest resolution: 12 Å
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 0 0 2156

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