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Yorodumi- EMDB-4043: 13-protofilament microtubule structure determined in situ from U8... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4043 | |||||||||
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Title | 13-protofilament microtubule structure determined in situ from U87MG cell | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 18.5 Å | |||||||||
Authors | Grange M / Vasishtan D / Gruenewald K | |||||||||
Citation | Journal: J Struct Biol / Year: 2017 Title: Cellular electron cryo tomography and in situ sub-volume averaging reveal the context of microtubule-based processes. Authors: Michael Grange / Daven Vasishtan / Kay Grünewald / Abstract: Electron cryo-tomography (cryoET) is currently the only technique that allows the direct observation of proteins in their native cellular environment. Sub-volume averaging of electron tomograms ...Electron cryo-tomography (cryoET) is currently the only technique that allows the direct observation of proteins in their native cellular environment. Sub-volume averaging of electron tomograms offers a route to increase the signal-to-noise of repetitive biological structures, such improving the information content and interpretability of tomograms. We discuss the potential for sub-volume averaging in highlighting and investigating specific processes in situ, focusing on microtubule structure and viral infection. We show that (i) in situ sub-volume averaging from single tomograms can guide and complement segmentation of biological features, (ii) the in situ determination of the structure of individual viruses is possible as they infect a cell, and (iii) novel, transient processes can be imaged with high levels of detail. | |||||||||
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_4043.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-4043-v30.xml emd-4043.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4043_fsc.xml | 3.4 KB | Display | FSC data file |
Images | emd_4043.png | 113.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4043 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4043 | HTTPS FTP |
-Validation report
Summary document | emd_4043_validation.pdf.gz | 289.3 KB | Display | EMDB validaton report |
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Full document | emd_4043_full_validation.pdf.gz | 288.4 KB | Display | |
Data in XML | emd_4043_validation.xml.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4043 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4043 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4043.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Microtubule
Entire | Name: Microtubule |
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Components |
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-Supramolecule #1: Microtubule
Supramolecule | Name: Microtubule / type: cell / ID: 1 / Parent: 0 / Details: Microtubule from U87MG cell |
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Source (natural) | Organism: Homo sapiens (human) / Strain: U87MG / Tissue: Cell |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 / Details: Cell |
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Grid | Model: C-flat 2/2 holey carbon gold supported grids (EMS) / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 60 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER Details: Adherent cells from on electron microscopy grid, manually blotted for 3s and plunge frozen. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 77.0 K / Max: 110.0 K |
Specialist optics | Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3836 pixel / Average electron dose: 1.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 4.0 µm / Calibrated magnification: 11848 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |