+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4487 | |||||||||
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Title | Structure of E. coli ribosome deposited by spraying | |||||||||
Map data | LocalRes filtered map | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Kontziampasis D / Klebl DP / Iadanza MG / Scarff CA / Kopf F / Sobott F / Monteiro DCF / Trebbin M / Muench SP / White HD | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: IUCrJ / Year: 2019 Title: A cryo-EM grid preparation device for time-resolved structural studies. Authors: Dimitrios Kontziampasis / David P Klebl / Matthew G Iadanza / Charlotte A Scarff / Florian Kopf / Frank Sobott / Diana C F Monteiro / Martin Trebbin / Stephen P Muench / Howard D White / Abstract: Structural biology generally provides static snapshots of protein conformations that can provide information on the functional mechanisms of biological systems. Time-resolved structural biology ...Structural biology generally provides static snapshots of protein conformations that can provide information on the functional mechanisms of biological systems. Time-resolved structural biology provides a means to visualize, at near-atomic resolution, the dynamic conformational changes that macromolecules undergo as they function. X-ray free-electron-laser technology has provided a powerful tool to study enzyme mechanisms at atomic resolution, typically in the femtosecond to picosecond timeframe. Complementary to this, recent advances in the resolution obtainable by electron microscopy and the broad range of samples that can be studied make it ideally suited to time-resolved approaches in the microsecond to millisecond timeframe to study large loop and domain motions in biomolecules. Here we describe a cryo-EM grid preparation device that permits rapid mixing, voltage-assisted spraying and vitrification of samples. It is shown that the device produces grids of sufficient ice quality to enable data collection from single grids that results in a sub-4 Å reconstruction. Rapid mixing can be achieved by blot-and-spray or mix-and-spray approaches with a delay of ∼10 ms, providing greater temporal resolution than previously reported mix-and-spray approaches. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4487.map.gz | 61.5 MB | EMDB map data format | |
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Header (meta data) | emd-4487-v30.xml emd-4487.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4487_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_4487.png | 84.4 KB | ||
Others | emd_4487_additional_1.map.gz emd_4487_additional_2.map.gz emd_4487_half_map_1.map.gz emd_4487_half_map_2.map.gz | 22.9 MB 79.7 MB 80.7 MB 80.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4487 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4487 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4487.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | LocalRes filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Sharpened map
File | emd_4487_additional_1.map | ||||||||||||
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Annotation | Sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_4487_additional_2.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap 1
File | emd_4487_half_map_1.map | ||||||||||||
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Annotation | halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap 2
File | emd_4487_half_map_2.map | ||||||||||||
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Annotation | halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ribosome from E. coli
Entire | Name: ribosome from E. coli |
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Components |
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-Supramolecule #1: ribosome from E. coli
Supramolecule | Name: ribosome from E. coli / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.9 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 66.0 e/Å2 |
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 |