+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16438 | |||||||||
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Title | Toroidal Dps-DNA assembly | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Co-crystal / DNA / Dps / biocrystallization / DNA BINDING PROTEIN | |||||||||
Biological species | Escherichia coli BL21(DE3) (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 22.0 Å | |||||||||
Authors | Chesnokov YM | |||||||||
Funding support | Russian Federation, 1 items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Morphological Diversity of Dps Complex with Genomic DNA. Authors: Yuri Chesnokov / Roman Kamyshinsky / Andrey Mozhaev / Eleonora Shtykova / Alexander Vasiliev / Ivan Orlov / Liubov Dadinova / Abstract: In response to adverse environmental factors, cells actively produce Dps proteins which form ordered complexes (biocrystals) with bacterial DNA to protect the genome. The effect of ...In response to adverse environmental factors, cells actively produce Dps proteins which form ordered complexes (biocrystals) with bacterial DNA to protect the genome. The effect of biocrystallization has been described extensively in the scientific literature; furthermore, to date, the structure of the Dps-DNA complex has been established in detail in vitro using plasmid DNA. In the present work, for the first time, Dps complexes with genomic DNA were studied in vitro using cryo-electron tomography. We demonstrate that genomic DNA forms one-dimensional crystals or filament-like assemblies which transform into weakly ordered complexes with triclinic unit cells, similar to what is observed for plasmid DNA. Changing such environmental factors as pH and KCl and MgCl concentrations leads to the formation of cylindrical structures. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16438.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-16438-v30.xml emd-16438.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16438_fsc.xml | 6 KB | Display | FSC data file |
Images | emd_16438.png | 176 KB | ||
Masks | emd_16438_msk_1.map | 8 MB | Mask map | |
Others | emd_16438_half_map_1.map.gz emd_16438_half_map_2.map.gz | 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16438 | HTTPS FTP |
-Validation report
Summary document | emd_16438_validation.pdf.gz | 1005.1 KB | Display | EMDB validaton report |
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Full document | emd_16438_full_validation.pdf.gz | 1004.6 KB | Display | |
Data in XML | emd_16438_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | emd_16438_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16438 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16438 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16438.map.gz / Format: CCP4 / Size: 8 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: 3.7 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16438_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16438_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16438_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dps-DNA assembly
Entire | Name: Dps-DNA assembly |
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Components |
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-Supramolecule #1: Dps-DNA assembly
Supramolecule | Name: Dps-DNA assembly / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 220 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 3D array |
-Sample preparation
Concentration | 3.1 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: 2.5 s blot. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 / Number real images: 2 / Average exposure time: 2.5 sec. / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 8.0 µm / Calibrated defocus min: 6.0 µm / Calibrated magnification: 37837 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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