+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4879 | |||||||||
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Title | QtEnc_E.coli | |||||||||
Map data | Map of QtEnc expressen in E.coli | |||||||||
Sample |
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Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Kube M / Westmeyer G | |||||||||
Citation | Journal: ACS Nano / Year: 2019 Title: Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters. Authors: Felix Sigmund / Susanne Pettinger / Massimo Kube / Fabian Schneider / Martina Schifferer / Steffen Schneider / Maria V Efremova / Jesús Pujol-Martí / Michaela Aichler / Axel Walch / Thomas ...Authors: Felix Sigmund / Susanne Pettinger / Massimo Kube / Fabian Schneider / Martina Schifferer / Steffen Schneider / Maria V Efremova / Jesús Pujol-Martí / Michaela Aichler / Axel Walch / Thomas Misgeld / Hendrik Dietz / Gil G Westmeyer / Abstract: Multicolored gene reporters for light microscopy are indispensable for biomedical research, but equivalent genetic tools for electron microscopy (EM) are still rare despite the increasing importance ...Multicolored gene reporters for light microscopy are indispensable for biomedical research, but equivalent genetic tools for electron microscopy (EM) are still rare despite the increasing importance of nanometer resolution for reverse engineering of molecular machinery and reliable mapping of cellular circuits. We here introduce the fully genetic encapsulin/cargo system of (Qt), which in combination with the recently characterized encapsulin system from (Mx) enables multiplexed gene reporter imaging conventional transmission electron microscopy (TEM) in mammalian cells. Cryo-electron reconstructions revealed that the Qt encapsulin shell self-assembles to nanospheres with = 4 icosahedral symmetry and a diameter of ∼43 nm harboring two putative pore regions at the 5-fold and 3-fold axes. We also found that upon heterologous expression in mammalian cells, the native cargo is autotargeted to the inner surface of the shell and exhibits ferroxidase activity leading to efficient intraluminal iron biomineralization, which enhances cellular TEM contrast. We furthermore demonstrate that the two differently sized encapsulins of Qt and Mx do not intermix and can be robustly differentiated by conventional TEM a deep learning classifier to enable automated multiplexed EM gene reporter imaging. | |||||||||
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_4879.map.gz | 223.5 MB | EMDB map data format | |
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Header (meta data) | emd-4879-v30.xml emd-4879.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4879_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_4879.png | 57 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4879 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4879 | HTTPS FTP |
-Validation report
Summary document | emd_4879_validation.pdf.gz | 354.1 KB | Display | EMDB validaton report |
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Full document | emd_4879_full_validation.pdf.gz | 353.3 KB | Display | |
Data in XML | emd_4879_validation.xml.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4879 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4879 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4879.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of QtEnc expressen in E.coli | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : QtEnc
Entire | Name: QtEnc |
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Components |
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-Supramolecule #1: QtEnc
Supramolecule | Name: QtEnc / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-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: 60.0 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 |