EMDB-11210: Structure of DPS determined by movement-free cryoEM with zero dos...

Basic information

• Entry: Database: EMDB / ID: EMD-11210
• Title: Structure of DPS determined by movement-free cryoEM with zero dose extrapolation
• Map data: Masked map obtained suing zero-dose extrapolation thru exponential firs to amplitudes and linear fit to phases. The map is sharpened by a B factor of -55 Angstrom^2.

Sample

• Complex: DNA protection during starvation protein (DPS)
  • Protein or peptide: DNA protection during starvation protein
• Ligand: water

• Keywords: DNA-BINDING PROTEIN / DNA BINDING PROTEIN

Function / homology

Function:

DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / response to stress / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding / identical protein binding / membrane / cytoplasm

Domain/homology:

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

Component:

DNA protection during starvation protein / DNA protection during starvation protein

• Biological species: Escherichia coli (E. coli)
• Method: single particle reconstruction / cryo EM / Resolution: 1.9 Å
• Authors: Naydenova K / Russo CJ

Funding support

United Kingdom, 1 items

Organization	Grant number	Country
Medical Research Council (MRC, United Kingdom)	MC UP 120117	United Kingdom

• Citation: Journal: Science / Year: 2020; Title: Cryo-EM with sub-1 Å specimen movement.; Authors: Katerina Naydenova / Peipei Jia / Christopher J Russo / ; Abstract: Most information loss in cryogenic electron microscopy (cryo-EM) stems from particle movement during imaging, which remains poorly understood. We show that this movement is caused by buckling and subsequent deformation of the suspended ice, with a threshold that depends directly on the shape of the frozen water layer set by the support foil. We describe a specimen support design that eliminates buckling and reduces electron beam-induced particle movement to less than 1 angstrom. The design allows precise foil tracking during imaging with high-speed detectors, thereby lessening demands on cryostage precision and stability. It includes a maximal density of holes, which increases throughput in automated cryo-EM without degrading data quality. Movement-free imaging allows extrapolation to a three-dimensional map of the specimen at zero electron exposure, before the onset of radiation damage.

History

Deposition	Jun 19, 2020	-
Header (metadata) release	Oct 21, 2020	-
Map release	Oct 21, 2020	-
Update	May 1, 2024	-
Current status	May 1, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_11210.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Masked map obtained suing zero-dose extrapolation thru exponential firs to amplitudes and linear fit to phases. The map is sharpened by a B factor of -55 Angstrom^2.
• Voxel size: X=Y=Z: 0.646 Å

Density

Contour Level	By AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum	-0.041407477 - 0.077251725
Average (Standard dev.)	0.000040034603 (±0.002644516)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 300 300 300 Spacing 300 300 300
Cell	A=B=C: 193.8 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	0.646	0.646	0.646
M x/y/z	300	300	300
origin x/y/z	0.000	0.000	0.000
length x/y/z	193.800	193.800	193.800
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	94	82	110
NX/NY/NZ	113	137	76
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	300	300	300
D min/max/mean	-0.041	0.077	0.000

Supplemental data

Mask #1

• File: emd_11210_msk_1.map

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Sample components

Entire : DNA protection during starvation protein (DPS)

• Entire: Name: DNA protection during starvation protein (DPS)

Components

• Complex: DNA protection during starvation protein (DPS)
  • Protein or peptide: DNA protection during starvation protein
• Ligand: water

Supramolecule #1: DNA protection during starvation protein (DPS)

• Supramolecule: Name: DNA protection during starvation protein (DPS) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
• Source (natural): Organism: Escherichia coli (E. coli)

Macromolecule #1: DNA protection during starvation protein

• Macromolecule: Name: DNA protection during starvation protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
• Source (natural): Organism: Escherichia coli (E. coli)
• Molecular weight: Theoretical: 18.720295 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

MSTAKLVKSK ATNLLYTRND VSDSEKKATV ELLNRQVIQF IDLSLITKQA HWNMRGANFI AVHEMLDGFR TALIDHLDTM AERAVQLGG VALGTTQVIN SKTPLKSYPL DIHNVQDHLK ELADRYAIVA NDVRKAIGEA KDDDTADILT AASRDLDKFL W FIESNIE

UniProtKB: DNA protection during starvation protein

Macromolecule #2: water

• Macromolecule: Name: water / type: ligand / ID: 2 / Number of copies: 964 / Formula: HOH
• Molecular weight: Theoretical: 18.015 Da

Chemical component information

ChemComp-HOH:
WATER

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.7
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 35.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: EMDB MAP
• Final reconstruction: Applied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 275623
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD