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Yorodumi- EMDB-16136: Cryo-electron tomogram acquired on a cryo-FIB lamella of a retina... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16136 | |||||||||
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Title | Cryo-electron tomogram acquired on a cryo-FIB lamella of a retinal pigment epithelial (RPE1) cell | |||||||||
Map data | Reconstructed cryo-electron tomogram acquired on RPE1 cryo-FIB lamella | |||||||||
Sample |
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Keywords | Actin stress fiber / CYTOSOLIC PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Mahamid J / Goetz SK | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nat Methods / Year: 2020 Title: Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies. Authors: Mauricio Toro-Nahuelpan / Ievgeniia Zagoriy / Fabrice Senger / Laurent Blanchoin / Manuel Théry / Julia Mahamid / Abstract: Spatially controlled cell adhesion on electron microscopy supports remains a bottleneck in specimen preparation for cellular cryo-electron tomography. Here, we describe contactless and mask-free ...Spatially controlled cell adhesion on electron microscopy supports remains a bottleneck in specimen preparation for cellular cryo-electron tomography. Here, we describe contactless and mask-free photo-micropatterning of electron microscopy grids for site-specific deposition of extracellular matrix-related proteins. We attained refined cell positioning for micromachining by cryo-focused ion beam milling. Complex micropatterns generated predictable intracellular organization, allowing direct correlation between cell architecture and in-cell three-dimensional structural characterization of the underlying molecular machinery. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16136.map.gz | 361.3 MB | EMDB map data format | |
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Header (meta data) | emd-16136-v30.xml emd-16136.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_16136.png | 342.6 KB | ||
Masks | emd_16136_msk_1.map | 2 GB | Mask map | |
Filedesc metadata | emd-16136.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16136 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16136 | HTTPS FTP |
-Validation report
Summary document | emd_16136_validation.pdf.gz | 778.7 KB | Display | EMDB validaton report |
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Full document | emd_16136_full_validation.pdf.gz | 778.3 KB | Display | |
Data in XML | emd_16136_validation.xml.gz | 3.4 KB | Display | |
Data in CIF | emd_16136_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16136 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16136 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16136.map.gz / Format: CCP4 / Size: 513.3 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
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Annotation | Reconstructed cryo-electron tomogram acquired on RPE1 cryo-FIB lamella | ||||||||||||||||||||
Voxel size | X=Y=Z: 13.481 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16136_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RPE1 cytosol with actin stress fiber
Entire | Name: RPE1 cytosol with actin stress fiber |
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Components |
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-Supramolecule #1: RPE1 cytosol with actin stress fiber
Supramolecule | Name: RPE1 cytosol with actin stress fiber / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Strain: RPE1 cell line / Location in cell: cytosol |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE |
Cryo protectant | None |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 120 / Focused ion beam - Temperature: 88 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200 Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Thermo Fisher Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 57 |
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