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- PDB-7en3: Crystal structure of tubulin in complex with Tubulysin analogue TGL -
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Open data
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Basic information
Entry | Database: PDB / ID: 7en3 | ||||||
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Title | Crystal structure of tubulin in complex with Tubulysin analogue TGL | ||||||
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![]() | STRUCTURAL PROTEIN/INHIBITOR / microtubule assembly inhibitors / STRUCTURAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() tubulin-tyrosine ligase activity / 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 ...tubulin-tyrosine ligase activity / 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 / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / positive regulation of axon guidance / COPI-mediated anterograde transport / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / Li, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The X-ray structure of tubulysin analogue TGL in complex with tubulin and three possible routes for the development of next-generation tubulysin analogues. Authors: Li, W. / Tan, L. / Zhang, Z. / Xia, Q. / Lei, D. / Li, Y. / Zhang, T. / Zeng, S. / Sima, X. / Wang, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 454.5 KB | Display | ![]() |
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PDB format | ![]() | 363.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 74.9 KB | Display | |
Data in CIF | ![]() | 102.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4i55S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 4 types, 6 molecules ACBDEF
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | | Mass: 16082.335 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | | Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 8 types, 172 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/J6R.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/J6R.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-ACP / | #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 6% PEG, 5% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2021 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.643→40.055 Å / Num. obs: 87655 / % possible obs: 98.44 % / Redundancy: 6.5 % / CC1/2: 0.872 / Net I/σ(I): 20.57 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I55 Resolution: 2.643→40.055 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.831 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.651 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.13 Å2 / Biso mean: 45.279 Å2 / Biso min: 16.03 Å2
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Refinement step | Cycle: final / Resolution: 2.643→40.055 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.643→2.711 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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