+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17958 | |||||||||||||||||||||
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Title | Structure of DPS determined by cryoEM at 100 keV | |||||||||||||||||||||
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Sample |
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Keywords | 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 / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / 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 | |||||||||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||||||||
Authors | McMullan 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
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17958.map.gz | 8.4 MB | EMDB map data format | |
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Header (meta data) | emd-17958-v30.xml emd-17958.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17958_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_17958.png | 102.2 KB | ||
Masks | emd_17958_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-17958.cif.gz | 6.1 KB | ||
Others | emd_17958_half_map_1.map.gz emd_17958_half_map_2.map.gz | 65.3 MB 65.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17958 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17958 | HTTPS FTP |
-Validation report
Summary document | emd_17958_validation.pdf.gz | 745.2 KB | Display | EMDB validaton report |
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Full document | emd_17958_full_validation.pdf.gz | 744.8 KB | Display | |
Data in XML | emd_17958_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_17958_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17958 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17958 | HTTPS FTP |
-Related structure data
Related structure data | 8pv9MC 8pvaC 8pvbC 8pvcC 8pvdC 8pveC 8pvfC 8pvgC 8pvhC 8pviC 8pvjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17958.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.862 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17958_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17958_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17958_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DNA protection during starvation protein (DPS)
Entire | Name: DNA protection during starvation protein (DPS) |
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Components |
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-Supramolecule #1: DNA protection during starvation protein (DPS)
Supramolecule | Name: DNA protection during starvation protein (DPS) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 1 / Enantiomer: LEVO / EC number: Oxidoreductases; Oxidizing metal ions |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 18.530996 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: STAKLVKSKA TNLLYTRNDV SDSEKAATVE LLNRQVIQFI DLSLITKQAH WNMRGANFIA VHEMLDGFRT ALIDHLDTMA ERAVQLGGV ALGTTQVINS KTPLKSYPLD IHNVQDHLKE LADRYAIVAN DVRKAIGEAK DDDTADILTA ASRDLDKFLW F IESNIE UniProtKB: DNA protection during starvation protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: UltrAuFoil R0./1 / Material: GOLD |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 1400/HR + YPS FEG |
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Image recording | Film 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 beam | Acceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |