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Yorodumi- EMDB-10195: Doublecortin N-terminal DC-domain (NDC)-decorated 13-protofilamen... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10195 | ||||||||||||||||||
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Title | Doublecortin N-terminal DC-domain (NDC)-decorated 13-protofilament microtubule (GDP state) processed with MiRP (Microtubule Relion-based Pipeline) | ||||||||||||||||||
Map data | C1 reconstruction of 13-protofilament GDP-microtubule decorated with NDC-NDC chimera of human doublecortin | ||||||||||||||||||
Sample |
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Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.5 Å | ||||||||||||||||||
Authors | Cook AC / Manka SW / Wang S / Moores CA / Atherton J | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: J Struct Biol / Year: 2020 Title: A microtubule RELION-based pipeline for cryo-EM image processing. Authors: Alexander D Cook / Szymon W Manka / Su Wang / Carolyn A Moores / Joseph Atherton / Abstract: Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall ...Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins. | ||||||||||||||||||
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_10195.map.gz | 245.8 MB | EMDB map data format | |
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Header (meta data) | emd-10195-v30.xml emd-10195.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_10195.png | 229.9 KB | ||
Others | emd_10195_additional.map.gz emd_10195_additional_1.map.gz | 488 KB 488 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10195 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10195 | HTTPS FTP |
-Validation report
Summary document | emd_10195_validation.pdf.gz | 308 KB | Display | EMDB validaton report |
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Full document | emd_10195_full_validation.pdf.gz | 307.1 KB | Display | |
Data in XML | emd_10195_validation.xml.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10195 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10195 | HTTPS FTP |
-Related structure data
Related structure data | 4862C 6rf8C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10300 (Title: Cryo micrographs of microtubules (GDP state) decorated with NDC-NDC chimera of human doublecortin Data size: 50.4 Data #1: Aligned movie frames of microtubules decorated with NDC-NDC chimera of human doublecortin [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10195.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | C1 reconstruction of 13-protofilament GDP-microtubule decorated with NDC-NDC chimera of human doublecortin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: None
File | emd_10195_additional.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: None
File | emd_10195_additional_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 13-protofilament microtubule decorated with NDC-NDC chimera of hu...
Entire | Name: 13-protofilament microtubule decorated with NDC-NDC chimera of human doublecortin |
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Components |
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-Supramolecule #1: 13-protofilament microtubule decorated with NDC-NDC chimera of hu...
Supramolecule | Name: 13-protofilament microtubule decorated with NDC-NDC chimera of human doublecortin type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 25.0 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: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Microtubule RELION-based pipeline (MiRP) |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 9.46 Å Applied symmetry - Helical parameters - Δ&Phi: -27.67 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33392 |
Final angle assignment | Type: NOT APPLICABLE |