+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9637 | |||||||||
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Title | 5R-MAP4, kinesin-1, and microtubule complex | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Bos taurus (cattle) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.29 Å | |||||||||
Authors | Shigematsu H / Imasaki T / Doki C / Sumi T / Aoki M / Uchikubo-Kamo T / Sakamoto A / Tokuraku K / Shirouzu M / Nitta R | |||||||||
Citation | Journal: J Cell Biol / Year: 2018 Title: Structural insight into microtubule stabilization and kinesin inhibition by Tau family MAPs. Authors: Hideki Shigematsu / Tsuyoshi Imasaki / Chihiro Doki / Takuya Sumi / Mari Aoki / Tomomi Uchikubo-Kamo / Ayako Sakamoto / Kiyotaka Tokuraku / Mikako Shirouzu / Ryo Nitta / Abstract: The Tau family microtubule-associated proteins (MAPs) promote microtubule stabilization and regulate microtubule-based motility. They share the C-terminal microtubule-binding domain, which includes ...The Tau family microtubule-associated proteins (MAPs) promote microtubule stabilization and regulate microtubule-based motility. They share the C-terminal microtubule-binding domain, which includes three to five tubulin-binding repeats. Different numbers of repeats formed by alternative splicing have distinct effects on the activities of these proteins, and the distribution of these variants regulates fundamental physiological phenomena in cells. In this study, using cryo-EM, we visualized the MAP4 microtubule complex with the molecular motor kinesin-1. MAP4 bound to the C-terminal domains of tubulins along the protofilaments stabilizes the longitudinal contacts of the microtubule. The strongest bond of MAP4 was found around the intertubulin-dimer interface such that MAP4 coexists on the microtubule with kinesin-1 bound to the intratubulin-dimer interface as well. MAP4, consisting of five repeats, further folds and accumulates above the intertubulin-dimer interface, interfering with kinesin-1 movement. Therefore, these cryo-EM studies reveal new insight into the structural basis of microtubule stabilization and inhibition of kinesin motility by the Tau family MAPs. | |||||||||
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_9637.map.gz | 13.6 MB | EMDB map data format | |
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Header (meta data) | emd-9637-v30.xml emd-9637.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_9637.png | 366.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9637 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9637 | HTTPS FTP |
-Validation report
Summary document | emd_9637_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_9637_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_9637_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9637 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9637 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9637.map.gz / Format: CCP4 / Size: 14.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.284 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-Kinesin-1-5R-MAP4 complex
Entire | Name: Microtubule-Kinesin-1-5R-MAP4 complex |
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Components |
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-Supramolecule #1: Microtubule-Kinesin-1-5R-MAP4 complex
Supramolecule | Name: Microtubule-Kinesin-1-5R-MAP4 complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Bos taurus (cattle) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)pLysS / Recombinant plasmid: pET21d |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 / Details: 100 mM PIPES-KOH at pH 6.8, 1 mM MgCl2, 1 mM EGTA |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Details | Alignment procedure by FEI User Interface Software. Not determined the residual tilt value. |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-34 / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 8.7 Å Applied symmetry - Helical parameters - Δ&Phi: -25.76 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 7.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15148 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Final angle assignment | Type: NOT APPLICABLE |