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- EMDB-19190: REEL analysis reconstructions of lumbricus terrestris erythrocruo... -
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Open data
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Basic information
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Title | REEL analysis reconstructions of lumbricus terrestris erythrocruorin (worm hemoglobin) | |||||||||
![]() | Reference reconstruction | |||||||||
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![]() | stem-eels / eels / reel-em / energy loss / single-particle / elemental mapping / elastic bright field / reconstructed energy loss / METAL BINDING PROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 27.0 Å | |||||||||
![]() | Pfeil-Gardiner O / Murphy BJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Elemental mapping in single-particle reconstructions by reconstructed electron energy-loss analysis. Authors: Olivia Pfeil-Gardiner / Higor Vinícius Dias Rosa / Dietmar Riedel / Yu Seby Chen / Dominique Lörks / Pirmin Kükelhan / Martin Linck / Heiko Müller / Filip Van Petegem / Bonnie J Murphy / ![]() ![]() Abstract: For macromolecular structures determined by cryogenic electron microscopy, no technique currently exists for mapping elements to defined locations, leading to errors in the assignment of metals and ...For macromolecular structures determined by cryogenic electron microscopy, no technique currently exists for mapping elements to defined locations, leading to errors in the assignment of metals and other ions, cofactors, substrates, inhibitors and lipids that play essential roles in activity and regulation. Elemental mapping in the electron microscope is well established for dose-tolerant samples but is challenging for biological samples, especially in a cryo-preserved state. Here we combine electron energy-loss spectroscopy with single-particle image processing to allow elemental mapping in cryo-preserved macromolecular complexes. Proof-of-principle data show that our method, reconstructed electron energy-loss (REEL) analysis, allows a three-dimensional reconstruction of electron energy-loss spectroscopy data, such that a high total electron dose is accumulated across many copies of a complex. Working with two test samples, we demonstrate that we can reliably localize abundant elements. We discuss the current limitations of the method and potential future developments. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.6 KB 22.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.9 KB | Display | ![]() |
Images | ![]() | 116.3 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 4.4 MB 4.4 MB 4.4 MB 6 MB 6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 675.6 KB | Display | ![]() |
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Full document | ![]() | 675.1 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reference reconstruction | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.65 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Energy-loss map before the carbon K-edge generated by...
File | emd_19190_additional_1.map | ||||||||||||
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Annotation | Energy-loss map before the carbon K-edge generated by summing REEL-EM maps in the energy range between and 237.5 eV to 242.1 eV. Best displayed with lowpass filtering. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Energy-loss map at the oxygen K-edge generated by...
File | emd_19190_additional_2.map | ||||||||||||
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Annotation | Energy-loss map at the oxygen K-edge generated by summing REEL-EM maps in the energy range between and 540.4 eV to 545.0 eV. Best displayed with lowpass filtering. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Energy-loss map at the carbon K-edge generated by...
File | emd_19190_additional_3.map | ||||||||||||
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Annotation | Energy-loss map at the carbon K-edge generated by summing REEL-EM maps in the energy range between and 283.2 eV to 287.8 eV. Best displayed with lowpass filtering. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Halfmap 1
File | emd_19190_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_19190_half_map_2.map | ||||||||||||
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Annotation | Halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Worm hemoglobin
Entire | Name: Worm hemoglobin |
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Components |
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-Supramolecule #1: Worm hemoglobin
Supramolecule | Name: Worm hemoglobin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.3 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Details: energy filter used in spectroscopy mode, so without a slit |
Details | The data were collected as STEM-EELS spectral images. |
Image recording | Film or detector model: DECTRIS ELA (1k x 0.5k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 1142 / Average electron dose: 92.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 0.0 µm / Calibrated defocus min: 0.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |