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Yorodumi- EMDB-41177: Protofilament reconstruction of microtubule decorated with Abl2-5... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41177 | |||||||||||||||||||||
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Title | Protofilament reconstruction of microtubule decorated with Abl2-557-1090, Class 3 | |||||||||||||||||||||
Map data | Gaussian smoothed map of protofilament reconstruction of microtubule decorated with Abl2-557-1090, Class 3 | |||||||||||||||||||||
Sample |
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Keywords | Microtubule / Abl2 / PROTEIN FIBRIL | |||||||||||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||||||||||||||
Authors | Lyu W / Duan D / Chai P | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Curr Biol / Year: 2023 Title: Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation. Authors: Daisy Duan / Wanqing Lyu / Pengxin Chai / Shaojie Ma / Kuanlin Wu / Chunxiang Wu / Yong Xiong / Nenad Sestan / Kai Zhang / Anthony J Koleske / Abstract: Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with ...Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation, both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics are unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo liquid-liquid phase separation (LLPS) and form co-condensates with tubulin. Abl2 binds to regions adjacent to MT damage, facilitates MT repair via fresh tubulin recruitment, and increases MT rescue frequency and lifetime. Cryo-EM analyses strongly support a model in which Abl2 engages tubulin C-terminal tails along an extended MT lattice conformation at damage sites to facilitate repair via fresh tubulin recruitment. Abl2Δ688-790, which closely mimics a naturally occurring splice isoform, retains binding to the MT lattice but does not bind tubulin, promote MT nucleation, or increase rescue frequency. In COS-7 cells, MT reassembly after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared with wild-type cells, and these defects are rescued by re-expression of Abl2, but not Abl2Δ688-790. We propose that Abl2 locally concentrates tubulin to promote MT nucleation and recruits it to defects in the MT lattice to enable repair and rescue. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41177.map.gz | 83.9 MB | EMDB map data format | |
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Header (meta data) | emd-41177-v30.xml emd-41177.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41177_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_41177.png | 32.8 KB | ||
Masks | emd_41177_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-41177.cif.gz | 4.4 KB | ||
Others | emd_41177_additional_1.map.gz emd_41177_half_map_1.map.gz emd_41177_half_map_2.map.gz | 89.7 MB 164.9 MB 164.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41177 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41177 | HTTPS FTP |
-Validation report
Summary document | emd_41177_validation.pdf.gz | 713.1 KB | Display | EMDB validaton report |
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Full document | emd_41177_full_validation.pdf.gz | 712.6 KB | Display | |
Data in XML | emd_41177_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | emd_41177_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41177 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41177 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41177.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Gaussian smoothed map of protofilament reconstruction of microtubule decorated with Abl2-557-1090, Class 3 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.6256 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41177_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Original map of protofilament reconstruction of microtubule decorated...
File | emd_41177_additional_1.map | ||||||||||||
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Annotation | Original map of protofilament reconstruction of microtubule decorated with Abl2-557-1090, Class 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of protofilament reconstruction of microtubule...
File | emd_41177_half_map_1.map | ||||||||||||
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Annotation | Half map A of protofilament reconstruction of microtubule decorated with Abl2-557-1090, Class 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of protofilament reconstruction of microtubule...
File | emd_41177_half_map_2.map | ||||||||||||
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Annotation | Half map B of protofilament reconstruction of microtubule decorated with Abl2-557-1090, Class 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Protofilament reconstruction of microtubule decorated with Abl2-5...
Entire | Name: Protofilament reconstruction of microtubule decorated with Abl2-557-1090 |
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Components |
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-Supramolecule #1: Protofilament reconstruction of microtubule decorated with Abl2-5...
Supramolecule | Name: Protofilament reconstruction of microtubule decorated with Abl2-557-1090 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: brain |
Molecular weight | Theoretical: 0.5 kDa/nm |
-Supramolecule #2: Abl2 C-terminals 557-1090
Supramolecule | Name: Abl2 C-terminals 557-1090 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 6.8 Details: 80 mM PIPES, pH 6.8, 1 mM MgCl2, 1 mM EGTA, 1 mM GMPCPP |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 36000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |