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Yorodumi- EMDB-5913: Cryo-electron tomography map of Leptospira interrogans flagellar ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5913 | |||||||||
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Title | Cryo-electron tomography map of Leptospira interrogans flagellar motor with 16-fold symmetry imposed | |||||||||
Map data | Reconstruction of Leptospira interrogans flagellar motor with 16-fold symmetry imposed | |||||||||
Sample |
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Keywords | flagellar motor / C ring / stator / Leptospira interrogans | |||||||||
Biological species | Leptospira interrogans (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 33.0 Å | |||||||||
Authors | Zhao XW / Norris SJ / Liu J | |||||||||
Citation | Journal: J Bacteriol / Year: 2012 Title: Three-dimensional structures of pathogenic and saprophytic Leptospira species revealed by cryo-electron tomography. Authors: Gianmarco Raddi / Dustin R Morado / Jie Yan / David A Haake / X Frank Yang / Jun Liu / Abstract: Leptospira interrogans is the primary causative agent of the most widespread zoonotic disease, leptospirosis. An in-depth structural characterization of L. interrogans is needed to understand its ...Leptospira interrogans is the primary causative agent of the most widespread zoonotic disease, leptospirosis. An in-depth structural characterization of L. interrogans is needed to understand its biology and pathogenesis. In this study, cryo-electron tomography (cryo-ET) was used to compare pathogenic and saprophytic species and examine the unique morphological features of this group of bacteria. Specifically, our study revealed a structural difference between the cell envelopes of L. interrogans and Leptospira biflexa involving variations in the lipopolysaccharide (LPS) layer. Through cryo-ET and subvolume averaging, we determined the first three-dimensional (3-D) structure of the flagellar motor of leptospira, with novel features in the flagellar C ring, export apparatus, and stator. Together with direct visualization of chemoreceptor arrays, DNA packing, periplasmic filaments, spherical cytoplasmic bodies, and a unique "cap" at the cell end, this report provides structural insights into these fascinating Leptospira species. | |||||||||
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_5913.map.gz | 44.4 MB | EMDB map data format | |
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Header (meta data) | emd-5913-v30.xml emd-5913.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_5913_fsc.xml | 7.5 KB | Display | FSC data file |
Images | emd_5913.jpeg emd_5913.tif | 86.2 KB 296.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5913 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5913 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5913.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Leptospira interrogans flagellar motor with 16-fold symmetry imposed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.7 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 : Flagellar motor of Leptospira interrogans
Entire | Name: Flagellar motor of Leptospira interrogans |
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Components |
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-Supramolecule #1000: Flagellar motor of Leptospira interrogans
Supramolecule | Name: Flagellar motor of Leptospira interrogans / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: FliY
Supramolecule | Name: FliY / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Leptospira interrogans (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
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-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -6.0 µm / Nominal defocus min: -4.0 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 ° |
Date | May 1, 2011 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 65 / Average electron dose: 100 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |