+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14948 | |||||||||
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Title | Dps nanocage with the "small circle" mineral core | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
Authors | Chesnokov YM / Kamyshinsky RA | |||||||||
Funding support | Russian Federation, 1 items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Structural Insights into Iron Ions Accumulation in Dps Nanocage. Authors: Yury Chesnokov / Andrey Mozhaev / Roman Kamyshinsky / Alexander Gordienko / Liubov Dadinova / Abstract: Dps (DNA-binding protein from starved cells) is well known for the structural protection of bacterial DNA by the formation of highly ordered intracellular assemblies under stress conditions. ...Dps (DNA-binding protein from starved cells) is well known for the structural protection of bacterial DNA by the formation of highly ordered intracellular assemblies under stress conditions. Moreover, this ferritin-like protein can perform fast oxidation of ferrous ions and subsequently accumulate clusters of ferric ions in its nanocages, thus providing the bacterium with physical and chemical protection. Here, cryo-electron microscopy was used to study the accumulation of iron ions in the nanocage of a Dps protein from . We demonstrate that Fe concentration in the solution and incubation time have an insignificant effect on the volume and the morphology of iron minerals formed in Dps nanocages. However, an increase in the Fe level leads to an increase in the proportion of larger clusters and the clusters themselves are composed of discrete ~1-1.5 nm subunits. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14948.map.gz | 28.7 MB | EMDB map data format | |
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Header (meta data) | emd-14948-v30.xml emd-14948.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14948_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_14948.png | 56.5 KB | ||
Masks | emd_14948_msk_1.map | 30.5 MB | Mask map | |
Others | emd_14948_half_map_1.map.gz emd_14948_half_map_2.map.gz | 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14948 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14948 | HTTPS FTP |
-Validation report
Summary document | emd_14948_validation.pdf.gz | 716.9 KB | Display | EMDB validaton report |
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Full document | emd_14948_full_validation.pdf.gz | 716.4 KB | Display | |
Data in XML | emd_14948_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_14948_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14948 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14948 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14948.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14948_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14948_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14948_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dps control
Entire | Name: Dps control |
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Components |
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-Supramolecule #1: Dps control
Supramolecule | Name: Dps control / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Molecular weight | Theoretical: 224 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.5 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 2.5 seconds. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 78.0 K / Max: 90.0 K |
Specialist optics | Spherical aberration corrector: Cs corrector by CEOS |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1419 / Average exposure time: 2.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 162790 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |