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Yorodumi- EMDB-16815: Tomogram of GBP1 coatomers assembled on brain polar lipid-derived... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16815 | |||||||||
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Title | Tomogram of GBP1 coatomers assembled on brain polar lipid-derived small unilamellar vesicles. | |||||||||
Map data | Electron cryotomogram of GBP1 coatomers on BPLE-derived SUVs. | |||||||||
Sample |
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Keywords | GBP1 / cryo-ET / liposome / coatomer / IMMUNE SYSTEM | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Kuhm TI / Jakobi AJ | |||||||||
Funding support | European Union, Netherlands, 2 items
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Citation | Journal: To Be Published Title: Structural basis of membrane targeting and coatomer formation by GBP1. Authors: Kuhm TI / de Agrela Pinto C / Huber S / Taisne C / Giannopoulou EA / Pardon E / Steyaert J / Jakobi AJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16815.map.gz | 1 GB | EMDB map data format | |
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Header (meta data) | emd-16815-v30.xml emd-16815.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_16815.png | 223.9 KB | ||
Masks | emd_16815_msk_1.map emd_16815_msk_2.map | 1.2 GB 1.2 GB | Mask map | |
Filedesc metadata | emd-16815.cif.gz | 4.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16815 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16815 | HTTPS FTP |
-Validation report
Summary document | emd_16815_validation.pdf.gz | 433.6 KB | Display | EMDB validaton report |
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Full document | emd_16815_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | emd_16815_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_16815_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16815 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16815 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16815.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Electron cryotomogram of GBP1 coatomers on BPLE-derived SUVs. | ||||||||||||||||||||
Voxel size | X=Y=Z: 6.15 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16815_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_16815_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 di...
Entire | Name: Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 dimers on brain polar lipid-derived SUVs. |
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Components |
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-Supramolecule #1: Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 di...
Supramolecule | Name: Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 dimers on brain polar lipid-derived SUVs. type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 20 K / Instrument: LEICA EM GP / Details: Blotted for 4 seconds from the carbon side.. |
Details | Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 dimers on brain polar lipid-derived SUVs. |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: CMC Utrecht / Diameter: 10 nm |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 61 / Average exposure time: 3.0 sec. / Average electron dose: 1.64 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 12000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Resolution method: OTHER / Software - Name: IMOD / Number images used: 61 |
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