+Open data
-Basic information
Entry | Database: PDB / ID: 6o2t | ||||||
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Title | Acetylated Microtubules | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / microtubule / cytoskeleton / acetylation | ||||||
Function / homology | Function and homology information Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Eshun-Wilson, L. / Zhang, R. / Portran, D. / Nachury, M.V. / Toso, D. / Lohr, T. / Vendruscolo, M. / Bonomi, M. / Fraser, J.S. / Nogales, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Effects of α-tubulin acetylation on microtubule structure and stability. Authors: Lisa Eshun-Wilson / Rui Zhang / Didier Portran / Maxence V Nachury / Daniel B Toso / Thomas Löhr / Michele Vendruscolo / Massimiliano Bonomi / James S Fraser / Eva Nogales / Abstract: Acetylation of K40 in α-tubulin is the sole posttranslational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule ...Acetylation of K40 in α-tubulin is the sole posttranslational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy (cryo-EM) reconstructions of pure samples of αTAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as a structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the flexible loop that contains αK40. Modification of αK40 reduces the disorder of the loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6o2t.cif.gz | 7.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6o2t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6o2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o2t_validation.pdf.gz | 8 MB | Display | wwPDB validaton report |
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Full document | 6o2t_full_validation.pdf.gz | 9.1 MB | Display | |
Data in XML | 6o2t_validation.xml.gz | 1.2 MB | Display | |
Data in CIF | 6o2t_validation.cif.gz | 1.8 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/6o2t ftp://data.pdbj.org/pub/pdb/validation_reports/o2/6o2t | HTTPS FTP |
-Related structure data
Related structure data | 0615MC 0612C 0613C 0614C 6o2qC 6o2rC 6o2sC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 52 / Rise per n subunits: 9.3 Å / Rotation per n subunits: -27.7 °) |
-Components
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: Brain / References: UniProt: Q2XVP4 #2: Protein | Mass: 49907.770 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: Brain / References: UniProt: P02554 #3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GDP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Acetylated Microtubule / Type: TISSUE / Entity ID: #1-#2 / Source: NATURAL | ||||||||||||||||||||
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Source (natural) | Organism: Sus scrofa (pig) / Tissue: Brain | ||||||||||||||||||||
Buffer solution | pH: 6.8 Details: Contains 80 mM PIPES, 1 mM MgCl2, 1 mM EGTA, pH 6.8 with KOH (stored at 4 degrees Celsius). | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Acetylated and deacetylated tubulin preparations were produced by treating purified brain tubulin with the acetyltransferase TAT1 or the tubulin deacetylatase SIRT2 as done in Portran et al. ...Details: Acetylated and deacetylated tubulin preparations were produced by treating purified brain tubulin with the acetyltransferase TAT1 or the tubulin deacetylatase SIRT2 as done in Portran et al. Nat. Cell. Bio. 2017. | ||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 310.15 K / Details: Blotted for 4 seconds at blot force 10. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: Preliminary grid screening was performed manually and all of the alignments were initially done using a gold calibration grid. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 23364 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1422.3 nm / Calibrated defocus max: 2706.1 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K |
Image recording | Average exposure time: 4 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 287 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 143 eV |
Image scans | Width: 3840 / Height: 3710 |
-Processing
EM software |
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CTF correction | Details: CTFFIND4 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -27.7 ° / Axial rise/subunit: 9.3 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 20256 / Details: Extracted Helical Segments | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18432 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 126 / Protocol: BACKBONE TRACE / Space: REAL / Target criteria: 0.5 Details: We use PHENIX to perform real space refinement and sharpen our cryoEM maps. | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3JAR Accession code: 3JAR / Source name: PDB / Type: experimental model |