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Yorodumi- EMDB-2939: Electron tomogram of Pseudomonas moraviensis stanleyae containing... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2939 | |||||||||
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Title | Electron tomogram of Pseudomonas moraviensis stanleyae containing selenium nanoparticles | |||||||||
Map data | Reconstruction of Pseudomonas moraviensis stanleyae containing selenium nanoparticles | |||||||||
Sample |
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Keywords | Pseudomonas moraviensis stanleyae / selenium nanoparticle / electron tomography | |||||||||
Method | electron tomography | |||||||||
Authors | Ni TW / Staicu L / Nemeth RS / Schwartz C / Crawford D / Seligman JD / Hunter WJ / Pilon-Smits E / Ackerson CJ | |||||||||
Citation | Journal: Nanoscale / Year: 2015 Title: Progress toward clonable inorganic nanoparticles. Authors: Thomas W Ni / Lucian C Staicu / Richard S Nemeth / Cindi L Schwartz / David Crawford / Jeffrey D Seligman / William J Hunter / Elizabeth A H Pilon-Smits / Christopher J Ackerson / Abstract: Pseudomonas moraviensis stanleyae was recently isolated from the roots of the selenium (Se) hyperaccumulator plant Stanleya pinnata. This bacterium tolerates normally lethal concentrations of SeO3(2-) ...Pseudomonas moraviensis stanleyae was recently isolated from the roots of the selenium (Se) hyperaccumulator plant Stanleya pinnata. This bacterium tolerates normally lethal concentrations of SeO3(2-) in liquid culture, where it also produces Se nanoparticles. Structure and cellular ultrastructure of the Se nanoparticles as determined by cellular electron tomography shows the nanoparticles as intracellular, of narrow dispersity, symmetrically irregular and without any observable membrane or structured protein shell. Protein mass spectrometry of a fractionated soluble cytosolic material with selenite reducing capability identified nitrite reductase and glutathione reductase homologues as NADPH dependent candidate enzymes for the reduction of selenite to zerovalent Se nanoparticles. In vitro experiments with commercially sourced glutathione reductase revealed that the enzyme can reduce SeO3(2-) (selenite) to Se nanoparticles in an NADPH-dependent process. The disappearance of the enzyme as determined by protein assay during nanoparticle formation suggests that glutathione reductase is associated with or possibly entombed in the nanoparticles whose formation it catalyzes. Chemically dissolving the nanoparticles releases the enzyme. The size of the nanoparticles varies with SeO3(2-) concentration, varying in size form 5 nm diameter when formed at 1.0 μM [SeO3(2-)] to 50 nm maximum diameter when formed at 100 μM [SeO3(2-)]. In aggregate, we suggest that glutathione reductase possesses the key attributes of a clonable nanoparticle system: ion reduction, nanoparticle retention and size control of the nanoparticle at the enzyme site. | |||||||||
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_2939.map.gz | 243.3 MB | EMDB map data format | |
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Header (meta data) | emd-2939-v30.xml emd-2939.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | EMD-2939.tif | 823.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2939 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2939 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2939.map.gz / Format: CCP4 / Size: 270.4 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Pseudomonas moraviensis stanleyae containing selenium nanoparticles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 91 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 : Selenium Nanoparticles contained within cells of Pseudomonas mora...
Entire | Name: Selenium Nanoparticles contained within cells of Pseudomonas moraviensis stanleyae |
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Components |
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-Supramolecule #1000: Selenium Nanoparticles contained within cells of Pseudomonas mora...
Supramolecule | Name: Selenium Nanoparticles contained within cells of Pseudomonas moraviensis stanleyae type: sample / ID: 1000 Details: Cells were grown in 10 mM HNaSeO3/LB for 36 hours. Medium was replaced every 8 hours. Number unique components: 1 |
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-Macromolecule #1: Pseudomonas moraviensis stanleyae
Macromolecule | Name: Pseudomonas moraviensis stanleyae / type: em_label / ID: 1 Details: ~80 nm selenium nanoparticles were made inside of Pseudomonas moraviensis stanleyae cells. Showing a potential clonable tag capable of making inorganic nanoparticles. |
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-Experimental details
-Structure determination
Processing | electron tomography |
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Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Details: 20 mM Tris, 2% glutaraldehyde, 2.5% formaldehyde |
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Grid | Details: Formvar coated copper slot grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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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 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 1 ° |
Date | Apr 12, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 120 |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: Etomo / Number images used: 120 |
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