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- PDB-3j6e: Energy minimized average structure of Microtubules stabilized by ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3j6e | ||||||
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Title | Energy minimized average structure of Microtubules stabilized by GmpCpp | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alushin, G.M. / Lander, G.C. / Kellogg, E.H. / Zhang, R. / Baker, D. / Nogales, E. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5895MC ![]() 5896C ![]() 5897C ![]() 5898C ![]() 5899C ![]() 3j6fC ![]() 3j6gC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Details | The 3 x 3 lattice represented in this entry is a segment of a microtubule. |
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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) ![]() ![]() ![]() #2: Protein | Mass: 47940.945 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 108 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/G2P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/G2P.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GTP / ![]() #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-G2P / #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: microtubule stabilized by GMPCPP / 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![]() ![]() |
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. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Apr 26, 2012 |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
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: 252 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction![]() | Details: ctftilt | ||||||||||||||||||||
3D reconstruction![]() | Method: projection matching / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57451 / 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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