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- EMDB-14949: Dps nanocage with the "dumbbell" mineral core -

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Basic information

Entry
Database: EMDB / ID: EMD-14949
TitleDps nanocage with the "dumbbell" mineral core
Map data
Sample
  • Organelle or cellular component: Dps control
Biological speciesEscherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.9 Å
AuthorsChesnokov YM / Kamyshinsky RA
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-04-00835 Russian Federation
CitationJournal: 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
DepositionMay 9, 2022-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateJun 8, 2022-
Current statusJun 8, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14949.png

Downloads & links

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Map

FileDownload / File: emd_14949.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 200 pix.
= 172. Å		0.86 Å/pix.
x 200 pix.
= 172. Å		0.86 Å/pix.
x 200 pix.
= 172. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.98776287 - 5.2240667
Average (Standard dev.)-0.014780904 (±0.14453739)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 172.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14949_msk_1.map
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Half map: #1

Fileemd_14949_half_map_1.map
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Half map: #2

Fileemd_14949_half_map_2.map
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Sample components

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Entire : Dps control

EntireName: Dps control
Components
  • Organelle or cellular component: Dps control

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Supramolecule #1: Dps control

SupramoleculeName: Dps control / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 224 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris-HCl
50.0 mMNaClNaCl
0.5 mMEDTAEDTA
5.0 mMFeSO4FeSO4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 2.5 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K / Max: 90.0 K
Specialist opticsSpherical aberration corrector: Cs corrector by CEOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen 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

Particle selectionNumber selected: 822217
CTF correctionSoftware - Name: Warp (ver. 1.0.9)
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 271765
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationNumber classes: 6 / Avg.num./class: 137036 / Software - Name: cryoSPARC (ver. 3.2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1dps

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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