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Yorodumi- EMDB-13881: CS-TV2-reconstructed tomogram of a C. crescentus stalk covered by... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13881 | |||||||||
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Title | CS-TV2-reconstructed tomogram of a C. crescentus stalk covered by an S-layer | |||||||||
Map data | CS-TV2 reconstruction of a C. crescentus stalk covered by an S-layer of RsaA hexamers. The tomogram was cropped and rotated to reduce file size. Contrast may require manual adjustment. | |||||||||
Sample |
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Keywords | S-layer / C. crescentus / RsaA / STRUCTURAL PROTEIN | |||||||||
Biological species | Caulobacter vibrioides (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Bharat TAM / Boehning J / Collins SM | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Structure / Year: 2022 Title: Compressed sensing for electron cryotomography and high-resolution subtomogram averaging of biological specimens. Authors: Jan Böhning / Tanmay A M Bharat / Sean M Collins / Abstract: Cryoelectron tomography (cryo-ET) and subtomogram averaging (STA) allow direct visualization and structural studies of biological macromolecules in their native cellular environment, in situ. Often, ...Cryoelectron tomography (cryo-ET) and subtomogram averaging (STA) allow direct visualization and structural studies of biological macromolecules in their native cellular environment, in situ. Often, low signal-to-noise ratios in tomograms, low particle abundance within the cell, and low throughput in typical cryo-ET workflows severely limit the obtainable structural information. To help mitigate these limitations, here we apply a compressed sensing approach using 3D second-order total variation (CS-TV) to tomographic reconstruction. We show that CS-TV increases the signal-to-noise ratio in tomograms, enhancing direct visualization of macromolecules, while preserving high-resolution information up to the secondary structure level. We show that, particularly with small datasets, CS-TV allows improvement of the resolution of STA maps. We further demonstrate that the CS-TV algorithm is applicable to cellular specimens, leading to increased visibility of molecular detail within tomograms. This work highlights the potential of compressed sensing-based reconstruction algorithms for cryo-ET and in situ structural biology. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13881.map.gz | 426.2 MB | EMDB map data format | |
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Header (meta data) | emd-13881-v30.xml emd-13881.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | emd_13881.png | 89.5 KB | ||
Filedesc metadata | emd-13881.cif.gz | 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13881 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13881 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13881.map.gz / Format: CCP4 / Size: 976 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CS-TV2 reconstruction of a C. crescentus stalk covered by an S-layer of RsaA hexamers. The tomogram was cropped and rotated to reduce file size. Contrast may require manual adjustment. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.467 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 : C. crescentus stalk
Entire | Name: C. crescentus stalk |
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Components |
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-Supramolecule #1: C. crescentus stalk
Supramolecule | Name: C. crescentus stalk / type: organelle_or_cellular_component / ID: 1 / Parent: 0 Details: C. crescentus stalk, covered by an S-layer of RsaA hexamers. |
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Source (natural) | Organism: Caulobacter vibrioides (bacteria) / Strain: CB15 / Location in cell: Stalk |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER/RHODIUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
Details | Please see Bharat et al, Nature Microbiology 2017 |
Cryo protectant | None |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: CMC Utrecht / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 3.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.578 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: IMOD Details: CS-TV2 reconstruction algorithm as described in manuscript was used. Number images used: 121 |
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-Atomic model buiding 1
Refinement | Protocol: OTHER |
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