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- EMDB-74453: Sub-tomogram averaged structure of E. Coli DNA protection during ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74453
TitleSub-tomogram averaged structure of E. Coli DNA protection during starvation protein (DPS)
Map data
Sample
  • Complex: DNA protection during starvation protein
    • Protein or peptide: DNA protection during starvation protein
  • Ligand: FE (III) ION
KeywordsDNA-binding / ferritin-like / DNA BINDING PROTEIN
Function / homology
Function and homology information


DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / response to stress / ferric iron binding / negative regulation of DNA-templated DNA replication initiation / DNA binding ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / response to stress / ferric iron binding / negative regulation of DNA-templated DNA replication initiation / DNA binding / membrane / identical protein binding / cytoplasm
Similarity search - Function
DNA protection during starvation protein, gammaproteobacteria / Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
DNA protection during starvation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 3.0 Å
AuthorsYang JE / Sibert BS / Montemayor EJ / Parrell D / Larson MR / Kumar A / Maindola P / Cai K / Wright ER
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104540 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM139168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM143854 United States
Department of Energy (DOE, United States)DE-SC0018409 United States
CitationJournal: To Be Published
Title: Sub-tomogram averaged structure of E. Coli DNA protection during starvation protein (DPS)
Authors: Yang JE / Sibert BS / Montemayor EJ / Parrell D / Larson MR / Kumar A / Maindola P / Cai K / Wright ER
History
DepositionDec 14, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74453.png

Downloads & links

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Map

FileDownload / File: emd_74453.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 168 pix.
= 199.92 Å		1.19 Å/pix.
x 168 pix.
= 199.92 Å		1.19 Å/pix.
x 168 pix.
= 199.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.097
Minimum - Maximum-0.3473663 - 0.5543292
Average (Standard dev.)-0.000000000000229 (±0.03352771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 199.92001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_74453_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74453_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA protection during starvation protein

EntireName: DNA protection during starvation protein
Components
  • Complex: DNA protection during starvation protein
    • Protein or peptide: DNA protection during starvation protein
  • Ligand: FE (III) ION

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Supramolecule #1: DNA protection during starvation protein

SupramoleculeName: DNA protection during starvation protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 225 KDa

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Macromolecule #1: DNA protection during starvation protein

MacromoleculeName: DNA protection during starvation protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: Oxidoreductases; Oxidizing metal ions
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.720295 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSTAKLVKSK ATNLLYTRND VSDSEKKATV ELLNRQVIQF IDLSLITKQA HWNMRGANFI AVHEMLDGFR TALIDHLDTM AERAVQLGG VALGTTQVIN SKTPLKSYPL DIHNVQDHLK ELADRYAIVA NDVRKAIGEA KDDDTADILT AASRDLDKFL W FIESNIE

UniProtKB: DNA protection during starvation protein

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7 / Details: 20 mM Tris, 100 mM NaCl, pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 1 / Average electron dose: 1.97 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
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

Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 9180
ExtractionNumber tomograms: 43 / Number images used: 31291 / Reference model: sub-tomogram from data sub-set / Method: manual / Software - Name: Dynamo
Details: A small set of DPS particles was manually picked from a single tomogram and aligned to produce an initial reference in Dynamo.
CTF correctionSoftware - Name: RELION (ver. 5.0) / Software - details: beta cu12.2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9zc2


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9znp:
Sub-tomogram averaged structure of E. Coli DNA protection during starvation protein (DPS)

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