+Open data
-Basic information
Entry | Database: PDB / ID: 3j6g | ||||||
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Title | Minimized average structure of microtubules stabilized by taxol | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / microtubule / taxol | ||||||
Function / homology | Function and homology information structural constituent of cytoskeleton / microtubule cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å | ||||||
Authors | Alushin, G.M. / Lander, G.C. / Kellogg, E.H. / Zhang, R. / Baker, D. / Nogales, E. | ||||||
Citation | Journal: Cell / Year: 2014 Title: High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Authors: Gregory M Alushin / Gabriel C Lander / Elizabeth H Kellogg / Rui Zhang / David Baker / Eva Nogales / Abstract: Dynamic instability, the stochastic switching between growth and shrinkage, is essential for microtubule function. This behavior is driven by GTP hydrolysis in the microtubule lattice and is ...Dynamic instability, the stochastic switching between growth and shrinkage, is essential for microtubule function. This behavior is driven by GTP hydrolysis in the microtubule lattice and is inhibited by anticancer agents like Taxol. We provide insight into the mechanism of dynamic instability, based on high-resolution cryo-EM structures (4.7-5.6 Å) of dynamic microtubules and microtubules stabilized by GMPCPP or Taxol. We infer that hydrolysis leads to a compaction around the E-site nucleotide at longitudinal interfaces, as well as movement of the α-tubulin intermediate domain and H7 helix. Displacement of the C-terminal helices in both α- and β-tubulin subunits suggests an effect on interactions with binding partners that contact this region. Taxol inhibits most of these conformational changes, allosterically inducing a GMPCPP-like state. Lateral interactions are similar in all conditions we examined, suggesting that microtubule lattice stability is primarily modulated at longitudinal interfaces. | ||||||
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 | 3j6g.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3j6g.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 3j6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j6g_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 3j6g_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 3j6g_validation.xml.gz | 234.5 KB | Display | |
Data in CIF | 3j6g_validation.cif.gz | 326.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/3j6g ftp://data.pdbj.org/pub/pdb/validation_reports/j6/3j6g | HTTPS FTP |
-Related structure data
Related structure data | 5897MC 5895C 5896C 5898C 5899C 3j6eC 3j6fC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Details | The 3 x 3 lattice represented in this entry is a segment of a microtubule. |
-Components
-Protein , 2 types, 18 molecules ACEGIKMOQBDFHJLNPR
#1: Protein | Mass: 48769.988 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550 #2: Protein | Mass: 47940.945 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554 |
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-Non-polymers , 5 types, 72 molecules
#3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GDP / #6: Chemical | ChemComp-TA1 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Microtubule stabilized by taxol / Type: COMPLEX |
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Buffer solution | Name: 80 mM PIPES, 1 mM EGTA, 1 mM MgCl2, 1 mM DTT, 0.05% Nonidet P-40 pH: 6.8 Details: 80 mM PIPES, 1 mM EGTA, 1 mM MgCl2, 1 mM DTT, 0.05% Nonidet P-40 |
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 400 mesh C-flat 1.2/1.3, glow discharged in Edwards carbon evaporator |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temp: 90.4 K / Humidity: 90 % Details: The grid was blotted for 2 seconds before plunging into liquid ethane (FEI VITROBOT MARK II). Method: The grid was blotted for 2 seconds before plunging. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: May 29, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 72000 X / Calibrated magnification: 72000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Gatan 626 holder / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 149 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: ctftilt | ||||||||||||||||||||
3D reconstruction | Method: projection matching / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24357 / Nominal pixel size: 1.74 Å / Actual pixel size: 1.74 Å / Symmetry type: HELICAL | ||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: REFINEMENT PROTOCOL--flexible fitting DETAILS--Structure represents the minimized average structure of the 1% lowest energy structures from the refinement run. | ||||||||||||||||||||
Atomic model building | PDB-ID: 1JFF Accession code: 1JFF / Source name: PDB / Type: experimental model | ||||||||||||||||||||
Refinement step | Cycle: LAST
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