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- EMDB-6683: The 7 angstrom resolution CryoEM map of the bacterial flagellar p... -

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Basic information

Entry
Database: EMDB / ID: EMD-6683
TitleThe 7 angstrom resolution CryoEM map of the bacterial flagellar polyrod
Map data
Sample
  • Complex: the bacterial flagellar polyrod
    • Protein or peptide: Flagellar basal-body rod protein FlgG
Keywordsthe bacterial flagellar motor / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar basal-body rod FlgG / 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 basal-body rod protein FlgG / Flagellar basal-body rod protein FlgG
Similarity search - Component
Biological speciesSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsFujii T / Namba K
CitationJournal: Nat Commun / Year: 2017
Title: Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook.
Authors: Takashi Fujii / Takayuki Kato / Koichi D Hiraoka / Tomoko Miyata / Tohru Minamino / Fabienne F V Chevance / Kelly T Hughes / Keiichi Namba /
Abstract: The bacterial flagellum is a motile organelle driven by a rotary motor, and its axial portions function as a drive shaft (rod), a universal joint (hook) and a helical propeller (filament). The rod ...The bacterial flagellum is a motile organelle driven by a rotary motor, and its axial portions function as a drive shaft (rod), a universal joint (hook) and a helical propeller (filament). The rod and hook are directly connected to each other, with their subunit proteins FlgG and FlgE having 39% sequence identity, but show distinct mechanical properties; the rod is straight and rigid as a drive shaft whereas the hook is flexible in bending as a universal joint. Here we report the structure of the rod and comparison with that of the hook. While these two structures have the same helical symmetry and repeat distance and nearly identical folds of corresponding domains, the domain orientations differ by ∼7°, resulting in tight and loose axial subunit packing in the rod and hook, respectively, conferring the rigidity on the rod and flexibility on the hook. This provides a good example of versatile use of a protein structure in biological organisms.
History
DepositionDec 2, 2016-
Header (metadata) releaseFeb 8, 2017-
Map releaseFeb 8, 2017-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.66
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.66
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wrh
  • Surface level: 1.66
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jzr
  • Surface level: 1.66
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5wrh
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jzr
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6683.png

Downloads & links

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Map

FileDownload / File: emd_6683.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 150 pix.
= 246. Å		1.64 Å/pix.
x 150 pix.
= 246. Å		1.64 Å/pix.
x 150 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.66 / Movie #1: 1.66
Minimum - Maximum-5.1757045 - 5.8002596
Average (Standard dev.)0.10676408 (±0.7893842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-75-75-75
Dimensions150150150
Spacing150150150
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z246.000246.000246.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-75-75-75
NC/NR/NS150150150
D min/max/mean-5.1765.8000.107

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Supplemental data

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Sample components

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Entire : the bacterial flagellar polyrod

EntireName: the bacterial flagellar polyrod
Components
  • Complex: the bacterial flagellar polyrod
    • Protein or peptide: Flagellar basal-body rod protein FlgG

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Supramolecule #1: the bacterial flagellar polyrod

SupramoleculeName: the bacterial flagellar polyrod / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Macromolecule #1: Flagellar basal-body rod protein FlgG

MacromoleculeName: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 27.784807 KDa
SequenceString: MISSLWIAKT GLDAQQTNMD VIANNLANVS TNGFKRQRAV FEDLLYQTIR QPGAQSSEQT TLPSGLQIGT GVRPVATERL HSQGNLSQT NNSKDVAIKG QGFFQVMLPD GTSAYTRDGS FQVDQNGQLV TAGGFQVQPA ITIPANALSI TIGRDGVVSV T QQGQAAPV ...String:
MISSLWIAKT GLDAQQTNMD VIANNLANVS TNGFKRQRAV FEDLLYQTIR QPGAQSSEQT TLPSGLQIGT GVRPVATERL HSQGNLSQT NNSKDVAIKG QGFFQVMLPD GTSAYTRDGS FQVDQNGQLV TAGGFQVQPA ITIPANALSI TIGRDGVVSV T QQGQAAPV QVGQLNLTTF MNDTGLESIG ENLYIETQSS GAPNESTPGL NGAGLLYQGY VETSNVNVAE ELVNMIQVQR AY EINSKAV STTDQMLQKL TQL

UniProtKB: Flagellar basal-body rod protein FlgG

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.13 Å
Applied symmetry - Helical parameters - Δ&Phi: 64.75 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 10645
Startup modelType of model: OTHER / Details: simple cylinder
Final angle assignmentType: NOT APPLICABLE

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