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- EMDB-1647: Specific arrangement of alpha-helical coiled coils in the core do... -

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Basic information

Entry
Database: EMDB / ID: EMD-1647
TitleSpecific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function
Map dataThis is a cryoEM map of the bacterial flagellar hook
Sample
  • Sample: Bacterial flagellar hook
  • Protein or peptide: Bacterial flagellar hook
KeywordsBacterial flagellum / flagellar hook / universal joint / electron cryomicroscopy / 3D image reconstruction
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytosol
Similarity search - Function
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, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal ...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, conserved site / Flagella basal body rod proteins signature. / 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 / Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsFujii T / Kato T / Namba K
CitationJournal: Structure / Year: 2009
Title: Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function.
Authors: Takashi Fujii / Takayuki Kato / Keiichi Namba /
Abstract: The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to ...The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to work as a universal joint. A partial atomic model of the hook revealed a sliding intersubunit domain interaction along the protofilament to produce bending flexibility. However, it remained unclear how the tightly packed inner core domains can still permit axial extension and compression. We report advances in cryoEM image analysis for high-resolution, high-throughput structural analysis and a density map of the hook that reveals most of the secondary structures, including the terminal alpha helices forming a coiled coil. The orientations and axial packing interactions of these two alpha helices are distinctly different from those of the filament, allowing them to have a room for axial compression and extension for bending flexibility without impairing the mechanical stability of the hook.
History
DepositionAug 26, 2009-
Header (metadata) releaseAug 28, 2009-
Map releaseNov 17, 2009-
UpdateApr 30, 2014-
Current statusApr 30, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.34
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.34
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3a69
  • Surface level: 0.34
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3a69
  • Surface level: 0.34
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6jzt
  • Surface level: 0.34
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jzt
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1647.jpg

Downloads & links

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Map

FileDownload / File: emd_1647.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cryoEM map of the bacterial flagellar hook
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 200 pix.
= 336. Å		1.68 Å/pix.
x 200 pix.
= 336. Å		1.68 Å/pix.
x 200 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34 / Movie #1: 0.34
Minimum - Maximum-1.55684316 - 2.13712454
Average (Standard dev.)0.00052996 (±0.2299886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-1.5572.1370.001

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Supplemental data

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Sample components

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Entire : Bacterial flagellar hook

EntireName: Bacterial flagellar hook
Components
  • Sample: Bacterial flagellar hook
  • Protein or peptide: Bacterial flagellar hook

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Supramolecule #1000: Bacterial flagellar hook

SupramoleculeName: Bacterial flagellar hook / type: sample / ID: 1000 / Oligomeric state: Bacterial flagellar hook / Number unique components: 1

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Macromolecule #1: Bacterial flagellar hook

MacromoleculeName: Bacterial flagellar hook / type: protein_or_peptide / ID: 1 / Name.synonym: Bacterial flagellar hook / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7 / Details: 20mM Tris-HCl, 100mM NaCl
GridDetails: Quantifoil holey carbon molybdenum grid R0.6/1.0
VitrificationCryogen name: HELIUM / Chamber humidity: 90 % / Chamber temperature: 4.6 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Vitorobot

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 50 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Specialist opticsEnergy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV
DateFeb 20, 2008
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 200 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 89285 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Top entry liquid helium-cooled cryo specimen holder
Specimen holder model: JEOL

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.12 Å
Applied symmetry - Helical parameters - Δ&Phi: 64.78 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
CTF correctionDetails: Each particle

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