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- EMDB-25437: Structure of DPSL (DNA Protection in Starved Cells - Like) from P... -

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Basic information

Entry
Database: EMDB / ID: EMD-25437
TitleStructure of DPSL (DNA Protection in Starved Cells - Like) from Pyrococcus furiosus
Map data
Sample
  • Complex: Dodecameric assembly of DPS-like protein
    • Protein or peptide: DNA protection during starvation protein
  • Ligand: ZINC ION
  • Ligand: FE (III) ION
  • Ligand: water
KeywordsDPS-like protein / METAL BINDING PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / DNA binding / cytoplasm
Similarity search - Function
: / DPS-like protein, ferritin-like diiron-binding domain / DNA-binding protein from starved cells-like / 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 speciesPyrococcus furiosus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsGauvin CC / Waghwani HK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DBI-1828765 United States
CitationJournal: To be published
Title: Structure of DPSL (DNA Protection in Starved Cells - Like) from Pyrococcus furiosus
Authors: Ramsay B / Wiedenheft B / Allen M / Gauss GH / Lawrence CM / Young M / Douglas T
History
DepositionNov 15, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7stw
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7stw
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25437.png

Downloads & links

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Map

FileDownload / File: emd_25437.map.gz / Format: CCP4 / Size: 2.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.15 Å/pix.
x 87 pix.
= 100.224 Å		1.15 Å/pix.
x 90 pix.
= 103.68 Å		1.15 Å/pix.
x 86 pix.
= 99.072 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.152 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.7
Minimum - Maximum-2.5488744 - 4.191737
Average (Standard dev.)0.000000000003336 (±0.48414382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin767977
Dimensions908687
Spacing879086
CellA: 100.224 Å / B: 103.67999 Å / C: 99.072 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1521.1521.152
M x/y/z879086
origin x/y/z0.0000.0000.000
length x/y/z100.224103.68099.072
α/β/γ90.00090.00090.000
start NX/NY/NZ777679
NX/NY/NZ879086
MAP C/R/S321
start NC/NR/NS797677
NC/NR/NS869087
D min/max/mean-2.5494.1920.000

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Supplemental data

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Half map: Half map 1

Fileemd_25437_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_25437_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dodecameric assembly of DPS-like protein

EntireName: Dodecameric assembly of DPS-like protein
Components
  • Complex: Dodecameric assembly of DPS-like protein
    • Protein or peptide: DNA protection during starvation protein
  • Ligand: ZINC ION
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: Dodecameric assembly of DPS-like protein

SupramoleculeName: Dodecameric assembly of DPS-like protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 256.32 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: Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 21.387254 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPEHNRRLVE RTGIDVEKLL ELLIKAAAAE FTTYYYYTIL RNHATGLEGE AIKEIIEDAR LEDRNHFEAL VPRIYELGGE LPRDIREFA DLASCRDAYL PEEPTIENIL KVLLEAERCA VGVYTEICNY TFGKDPRTYD LALAILHEEI EHEAWFEELL T GKPSGHFR RGKPGESPYV SKFLKTR

UniProtKB: DNA protection during starvation protein

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 257 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
120.0 mMNaClSodium chloride
20.0 mM(HOCH2)3CNH2Tris
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 5 Blot time 4.

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Electron microscopy

MicroscopeTFS TALOS
TemperatureMin: 77.0 K / Max: 100.0 K
DetailsBeam tilt was performed with a 3x3 matrix with corners omitted.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1574 / Average exposure time: 7.0 sec. / Average electron dose: 65.0 e/Å2 / Details: Images were dose-fractionated to have 50 frames
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.62 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsImages were gain normalized in SerialEM
Particle selectionNumber selected: 1812595
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 436835
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.2) / Software - details: Ab-initio
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.2)
Details: cryoSPARC "homogenous refinement" job that utilizes "Branch and Bound" refinement technique
Final 3D classificationNumber classes: 1 / Avg.num./class: 436835 / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2clb


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsWorkflow involved generating a homology model from 2CLB structure from S. solfataricus with the Pf sequence, using Swiss Model. Then, that homology model was fit to the map density initially in Chimera using fitmap. After that, it was initially refined with rigid body real-space refinement in Phenix, tuned in coot, and subsequently finished refining with flexible fitting and enforced tetrahedral symmetry.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-7stw:
Structure of DPSL (DNA Protection in Starved Cells - Like) from Pyrococcus furiosus

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