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- PDB-9znp: Sub-tomogram averaged structure of E. Coli DNA protection during ... -

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Basic information

Entry
Database: PDB / ID: 9znp
TitleSub-tomogram averaged structure of E. Coli DNA protection during starvation protein (DPS)
ComponentsDNA protection during starvation protein
KeywordsDNA BINDING PROTEIN / DNA-binding / ferritin-like
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)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 3 Å
AuthorsYang, J.E. / Sibert, B.S. / Montemayor, E.J. / Parrell, D. / Larson, M.R. / Kumar, A. / Maindola, P. / Cai, K. / Wright, E.R.
Funding support United States, 4items
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, J.E. / Sibert, B.S. / Montemayor, E.J. / Parrell, D. / Larson, M.R. / Kumar, A. / Maindola, P. / Cai, K. / Wright, E.R.
History
DepositionDec 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
G: DNA protection during starvation protein
H: DNA protection during starvation protein
I: DNA protection during starvation protein
J: DNA protection during starvation protein
K: DNA protection during starvation protein
L: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,31424
Polymers224,64412
Non-polymers67012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
DNA protection during starvation protein


Mass: 18720.295 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dps, pexB, vtm, b0812, JW0797 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ABT2, Oxidoreductases; Oxidizing metal ions
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: DNA protection during starvation protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.225 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7 / Details: 20 mM Tris, 100 mM NaCl, pH 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.97 e/Å2 / Avg electron dose per subtomogram: 80 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 1
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Dynamovolume selection
2SerialEM4.1.0image acquisitionbeta
4RELION5CTF correctionbeta cu12.2
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9180 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionMethod: manual
Details: A small set of DPS particles was manually picked from a single tomogram and aligned to produce an initial reference in Dynamo.
Num. of tomograms: 43 / Num. of volumes extracted: 31291 / Reference model: sub-tomogram from data sub-set
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 9ZC2

9zc2


Accession code: 9ZC2 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00814124
ELECTRON MICROSCOPYf_angle_d0.63719296
ELECTRON MICROSCOPYf_dihedral_angle_d4.1931968
ELECTRON MICROSCOPYf_chiral_restr0.0482364
ELECTRON MICROSCOPYf_plane_restr0.0052508

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