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Yorodumi- EMDB-5007: Divergence of Quaternary Structures among Bacterial Flagellar Fil... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5007 | |||||||||
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Title | Divergence of Quaternary Structures among Bacterial Flagellar Filaments | |||||||||
Map data | Volume | |||||||||
Sample |
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Keywords | flagellar filament / structural polymorphism / IHRSR | |||||||||
Biological species | Campylobacter jejuni (Campylobacter) | |||||||||
Method | helical reconstruction / cryo EM | |||||||||
Authors | Galkin VE / Yu X / Bielnicki J / Heuser J / Ewing CP / Guerry P / Egelman EH | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5007.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-5007-v30.xml emd-5007.xml | 6.8 KB 6.8 KB | Display Display | EMDB header |
Images | emd_5007_1.png | 123.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5007 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5007 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5007.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Volume | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Campylobacter jejuni flagellar filament
Entire | Name: Campylobacter jejuni flagellar filament |
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Components |
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-Supramolecule #1000: Campylobacter jejuni flagellar filament
Supramolecule | Name: 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
Supramolecule | Name: flagellar filament / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Campylobacter jejuni (Campylobacter) / Organelle: Flagella |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied 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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