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- EMDB-17958: Structure of DPS determined by cryoEM at 100 keV -

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Basic information

Entry
Database: EMDB / ID: EMD-17958
TitleStructure of DPS determined by cryoEM at 100 keV
Map data
Sample
  • Complex: DNA protection during starvation protein (DPS)
    • Protein or peptide: DNA protection during starvation protein
KeywordsDNA 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 / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis ...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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMcMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y ...McMullan G / Naydenova K / Mihaylov D / Peet MJ / Wilson H / Yamashita K / Dickerson JL / Chen S / Cannone G / Lee Y / Hutchings KA / Gittins O / Sobhy M / Wells T / El-Gomati MM / Dalby J / Meffert M / Schulze-Briese C / Henderson R / Russo CJ
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC UP 120117 United Kingdom
Medical Research Council (MRC, United Kingdom)MC U105184322 United Kingdom
Wellcome Trust220526/B/20/Z United Kingdom
Engineering and Physical Sciences Research CouncilR122522 United Kingdom
Innovate UK103806 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T003677/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure determination by cryoEM at 100 keV.
Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A ...Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A Hutchings / Olivia Gittins / Mohamed A Sobhy / Torquil Wells / Mohamed M El-Gomati / Jason Dalby / Matthias Meffert / Clemens Schulze-Briese / Richard Henderson / Christopher J Russo /
Abstract: Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose- ...Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.
History
DepositionJul 17, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17958.png

Downloads & links

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Map

FileDownload / File: emd_17958.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 280 pix.
= 241.36 Å		0.86 Å/pix.
x 280 pix.
= 241.36 Å		0.86 Å/pix.
x 280 pix.
= 241.36 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.092403494 - 0.1483443
Average (Standard dev.)0.000040863928 (±0.0048868507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 241.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17958_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_17958_half_map_1.map
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Histogram

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Half map: #2

Fileemd_17958_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : DNA protection during starvation protein (DPS)

EntireName: DNA protection during starvation protein (DPS)
Components
  • Complex: DNA protection during starvation protein (DPS)
    • Protein or peptide: DNA protection during starvation protein

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

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

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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: 1 / Enantiomer: LEVO / EC number: Oxidoreductases; Oxidizing metal ions
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.530996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
STAKLVKSKA TNLLYTRNDV SDSEKAATVE LLNRQVIQFI DLSLITKQAH WNMRGANFIA VHEMLDGFRT ALIDHLDTMA ERAVQLGGV ALGTTQVINS KTPLKSYPLD IHNVQDHLKE LADRYAIVAN DVRKAIGEAK DDDTADILTA ASRDLDKFLW F IESNIE

UniProtKB: DNA protection during starvation protein

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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

BufferpH: 7.5
GridModel: UltrAuFoil R0./1 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 1400/HR + YPS FEG
Image recordingFilm or detector model: DECTRIS SINGLA (1k x 1k) / Digitization - Dimensions - Width: 1030 pixel / Digitization - Dimensions - Height: 1066 pixel / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

13256

Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48896
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6zgl


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL
Output model

PDB-8pv9:
Structure of DPS determined by cryoEM at 100 keV

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