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- EMDB-16439: Dps-DNA filament-like assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-16439
TitleDps-DNA filament-like 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: 30.5 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_16439.png

Downloads & links

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Map

FileDownload / File: emd_16439.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 96 pix.
= 355.2 Å		3.7 Å/pix.
x 96 pix.
= 355.2 Å		3.7 Å/pix.
x 96 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-15.635261 - 56.186419999999998
Average (Standard dev.)1.3450047 (±5.7157426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16439_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_16439_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_16439_half_map_2.map
Projections & Slices
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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 statefilament

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Sample preparation

Concentration3.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
50.0 mMKClPotassium chloride
2.0 mMMgCl2Magnesium chloride
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
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
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 FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 30.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.1) / Number subtomograms used: 52
ExtractionNumber tomograms: 1 / Number images used: 52 / Method: manual / Software - Name: RELION (ver. 4.1)
Final 3D classificationNumber classes: 1 / Avg.num./class: 52 / Software - Name: RELION (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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