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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10286 | |||||||||
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Title | Cubic Dps-DNA crystal structure in vitro | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.7 Å | |||||||||
![]() | Chesnokov YM / Kamyshinsky RA / Vasiliev AL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Polymorphic Protective Dps-DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering. Authors: Roman Kamyshinsky / Yury Chesnokov / Liubov Dadinova / Andrey Mozhaev / Ivan Orlov / Maxim Petoukhov / Anton Orekhov / Eleonora Shtykova / Alexander Vasiliev / ![]() Abstract: Rapid increase of intracellular synthesis of specific histone-like Dps protein that binds DNA to protect the genome against deleterious factors leads to in cellulo crystallization-one of the most ...Rapid increase of intracellular synthesis of specific histone-like Dps protein that binds DNA to protect the genome against deleterious factors leads to in cellulo crystallization-one of the most curious processes in the area of life science at the moment. However, the actual structure of the Dps-DNA co-crystals remained uncertain in the details for more than two decades. Cryo-electron tomography and small-angle X-ray scattering revealed polymorphous modifications of the co-crystals depending on the buffer parameters. Two different types of the Dps-DNA co-crystals are formed in vitro: triclinic and cubic. Three-dimensional reconstruction revealed DNA and Dps molecules in cubic co-crystals, and the unit cell parameters of cubic lattice were determined consistently by both methods. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 3.3 KB | Display | ![]() |
Images | ![]() | 168.1 KB | ||
Masks | ![]() | 2.8 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 1.9 MB 1.9 MB 1.9 MB 1.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 398.7 KB | Display | ![]() |
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Full document | ![]() | 397.8 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 3.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Map before any post-processing
File | emd_10286_additional.map | ||||||||||||
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Annotation | Map before any post-processing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map before any post-processing
File | emd_10286_additional_1.map | ||||||||||||
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Annotation | Map before any post-processing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10286_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10286_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dps-DNA co-crystal
Entire | Name: Dps-DNA co-crystal |
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Components |
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-Supramolecule #1: Dps-DNA co-crystal
Supramolecule | Name: Dps-DNA co-crystal / type: complex / ID: 1 / Parent: 0 Details: Dps protein and DNA were mixed in the concentrations corresponding to the Dps/DNA ratio 1Dps dodecamer/60 bp of DNA. A ring vector pcDNA-hIRR-GFP 9900 bp was used as DNA sample. |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 224 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | 3D array |
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Sample preparation
Concentration | 3.1 mg/mL | ||||||
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Buffer | pH: 7.5 / Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 1.5 seconds. | ||||||
Details | weight Dps/DNA ratio = 3/1 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Cs image corrector (CEOS, Germany) |
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 / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 1.02 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 37837 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |