+Open data
-Basic information
Entry | Database: PDB / ID: 5yls | ||||||
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Title | Crystal structure of T2R-TTL-Y50 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / colchicine binding domain / tubulin inhibitor / tublin / Millepachine | ||||||
Function / homology | Function and homology information 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 / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Recruitment of NuMA to mitotic centrosomes / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Rattus norvegicus (Norway rat) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Yang, J.H. / Chen, L.J. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The compound millepachine and its derivatives inhibit tubulin polymerization by irreversibly binding to the colchicine-binding site in beta-tubulin. Authors: Yang, J.H. / Yan, W. / Yu, Y.M. / Wang, Y.X. / Yang, T. / Xue, L.L. / Yuan, X. / Long, C.F. / Liu, Z.W. / Chen, X.X. / Hu, M.S. / Zheng, L. / Qiu, Q. / Pei, H.Y. / Li, D. / Wang, F. / Bai, P. ...Authors: Yang, J.H. / Yan, W. / Yu, Y.M. / Wang, Y.X. / Yang, T. / Xue, L.L. / Yuan, X. / Long, C.F. / Liu, Z.W. / Chen, X.X. / Hu, M.S. / Zheng, L. / Qiu, Q. / Pei, H.Y. / Li, D. / Wang, F. / Bai, P. / Wen, J.L. / Ye, H.Y. / Chen, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yls.cif.gz | 450.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yls.ent.gz | 360.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/5yls ftp://data.pdbj.org/pub/pdb/validation_reports/yl/5yls | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Sus scrofa (pig) / Gene: TUBA1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q2XVP4 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBB2B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A287AGU7, UniProt: P02554*PLUS #3: Protein | | Mass: 16844.162 Da / Num. of mol.: 1 / Fragment: UNP residues 49-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043 #4: Protein | | Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43 |
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-Non-polymers , 9 types, 34 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-GOL / | #9: Chemical | ChemComp-GDP / | #10: Chemical | ChemComp-MES / | #11: Chemical | #12: Chemical | ChemComp-ACP / | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 6% polyethylene glycol 4000, 8% glycerol, 0.1M MES, 30mM CaCl2, 30mM MgCl2, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97845 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 62464 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 3→3.07 Å |
-Processing
Software |
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Refinement | Resolution: 3→45.788 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU B: 19.195 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 75.235 Å2
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Refinement step | Cycle: 1 / Resolution: 3→45.788 Å
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