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- EMDB-5007: Divergence of Quaternary Structures among Bacterial Flagellar Fil... -

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Basic information

Entry
Database: EMDB / ID: EMD-5007
TitleDivergence of Quaternary Structures among Bacterial Flagellar Filaments
Map dataVolume
Sample
  • Sample: Campylobacter jejuni flagellar filament
  • Organelle or cellular component: flagellar filament
Keywordsflagellar filament / structural polymorphism / IHRSR
Biological speciesCampylobacter jejuni (Campylobacter)
Methodhelical reconstruction / cryo EM
AuthorsGalkin VE / Yu X / Bielnicki J / Heuser J / Ewing CP / Guerry P / Egelman EH
CitationJournal: Science / Year: 2008
Title: Divergence of quaternary structures among bacterial flagellar filaments.
Authors: Vitold E Galkin / Xiong Yu / Jakub Bielnicki / John Heuser / Cheryl P Ewing / Patricia Guerry / Edward H Egelman /
Abstract: It has been widely assumed that the atomic structure of the flagellar filament from Salmonella typhimurium serves as a model for all bacterial flagellar filaments given the sequence conservation in ...It has been widely assumed that the atomic structure of the flagellar filament from Salmonella typhimurium serves as a model for all bacterial flagellar filaments given the sequence conservation in the coiled-coil regions responsible for polymerization. On the basis of electron microscopic images, we show that the flagellar filaments from Campylobacter jejuni have seven protofilaments rather than the 11 in S. typhimurium. The vertebrate Toll-like receptor 5 (TLR5) recognizes a region of bacterial flagellin that is involved in subunit-subunit assembly in Salmonella and many other pathogenic bacteria, and this short region has diverged in Campylobacter and related bacteria, such as Helicobacter pylori, which are not recognized by TLR5. The driving force in the change of quaternary structure between Salmonella and Campylobacter may have been the evasion of TLR5.
History
DepositionMar 6, 2008-
Header (metadata) releaseApr 21, 2008-
Map releaseApr 22, 2009-
UpdateMar 2, 2016-
Current statusMar 2, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.118
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.118
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5007_1.png

Downloads & links

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Map

FileDownload / File: emd_5007.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 100 pix.
= 240. Å		2.4 Å/pix.
x 100 pix.
= 240. Å		2.4 Å/pix.
x 100 pix.
= 240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.118 / Movie #1: 0.118
Minimum - Maximum-0.23480536 - 0.39745471
Average (Standard dev.)0.00967519 (±0.10778536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 240.00002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z240.000240.000240.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.2350.3970.010

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Supplemental data

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Sample components

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Entire : Campylobacter jejuni flagellar filament

EntireName: Campylobacter jejuni flagellar filament
Components
  • Sample: Campylobacter jejuni flagellar filament
  • Organelle or cellular component: flagellar filament

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Supramolecule #1000: Campylobacter jejuni flagellar filament

SupramoleculeName: Campylobacter jejuni flagellar filament / type: sample / ID: 1000 / Details: None / Oligomeric state: helical polymer / Number unique components: 1

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Supramolecule #1: flagellar filament

SupramoleculeName: flagellar filament / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Campylobacter jejuni (Campylobacter) / Organelle: Flagella

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 7.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 103.11 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER

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