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Yorodumi- EMDB-15467: In situ subtomogram average of floating microtubule inner protein... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15467 | |||||||||
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Title | In situ subtomogram average of floating microtubule inner protein 15 (fMIP15) | |||||||||
Map data | In situ subtomogram average of floating microtubule inner protein 15 | |||||||||
Sample |
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Keywords | microtubule associated protein / STRUCTURAL PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Chakraborty S / Mahamid J / Martinez-Sanchez A / Baumeister W | |||||||||
Funding support | 1 items
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Citation | Journal: Biorxiv / Year: 2024 Title: Cryo-electron tomography suggests tubulin chaperones form a subset of microtubule lumenal particles with a role in maintaining neuronal microtubules Authors: Chakraborty S / Martinez-Sanchez A / Beck F / Toro-Nahuelpan M / Hwang IY / Noh KM / Baumeister W / Mahamid J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15467.map.gz | 6.3 MB | EMDB map data format | |
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Header (meta data) | emd-15467-v30.xml emd-15467.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15467_fsc.xml | 4.7 KB | Display | FSC data file |
Images | emd_15467.png | 10 KB | ||
Filedesc metadata | emd-15467.cif.gz | 4.1 KB | ||
Others | emd_15467_half_map_1.map.gz emd_15467_half_map_2.map.gz | 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15467 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15467 | HTTPS FTP |
-Validation report
Summary document | emd_15467_validation.pdf.gz | 840.7 KB | Display | EMDB validaton report |
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Full document | emd_15467_full_validation.pdf.gz | 840.3 KB | Display | |
Data in XML | emd_15467_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_15467_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15467 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15467 | 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_15467.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | In situ subtomogram average of floating microtubule inner protein 15 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.129 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: In situ subtomogram average of floating microtubule inner protein 15
File | emd_15467_half_map_1.map | ||||||||||||
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Annotation | In situ subtomogram average of floating microtubule inner protein 15 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: In situ subtomogram average of floating microtubule inner protein 15
File | emd_15467_half_map_2.map | ||||||||||||
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Annotation | In situ subtomogram average of floating microtubule inner protein 15 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : fMIP15 from human induced pluripotent stem cells derived neuronal...
Entire | Name: fMIP15 from human induced pluripotent stem cells derived neuronal microtubules |
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Components |
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-Supramolecule #1: fMIP15 from human induced pluripotent stem cells derived neuronal...
Supramolecule | Name: fMIP15 from human induced pluripotent stem cells derived neuronal microtubules type: cell / 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 | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: Quantifoil / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Chamber temperature: 310 K / Instrument: LEICA EM GP |
Details | Frozen hydrated human induced pluripotent stem cells derived neuron |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K |
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: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |