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- EMDB-16438: Toroidal Dps-DNA assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-16438
TitleToroidal Dps-DNA assembly
Map data
Sample
  • Complex: Dps-DNA assembly
KeywordsCo-crystal / DNA / Dps / biocrystallization / DNA BINDING PROTEIN
Biological speciesEscherichia coli BL21(DE3) (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 22.0 Å
AuthorsChesnokov YM
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation18-74-10071 Russian Federation
CitationJournal: 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
DepositionJan 9, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16438.png

Downloads & links

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Map

FileDownload / File: emd_16438.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 128 pix.
= 473.6 Å		3.7 Å/pix.
x 128 pix.
= 473.6 Å		3.7 Å/pix.
x 128 pix.
= 473.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-51.417589999999997 - 45.07649
Average (Standard dev.)0.9839729 (±5.832656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 473.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16438_msk_1.map
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Half map: #1

Fileemd_16438_half_map_1.map
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Half map: #2

Fileemd_16438_half_map_2.map
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Sample components

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Entire : Dps-DNA assembly

EntireName: Dps-DNA assembly
Components
  • Complex: Dps-DNA assembly

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Supramolecule #1: Dps-DNA assembly

SupramoleculeName: Dps-DNA assembly / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 220 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

Concentration3.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTrisTris-HClTris
50.0 mMNaClSodium chlorideNaClSodium chloride
0.5 mMEDTAEthylenediaminetetraacetic acidEDTAEthylenediaminetetraacetic acid
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: 2.5 s blot.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 6 / Number images used: 717 / Method: manual / Software - Name: RELION (ver. 4.1)
Final 3D classificationNumber classes: 1 / Avg.num./class: 717 / Software - Name: RELION (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.1) / Number subtomograms used: 717
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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