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Yorodumi- PDB-5jqg: An apo tubulin-RB-TTL complex structure used for side-by-side com... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5jqg | ||||||
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| Title | An apo tubulin-RB-TTL complex structure used for side-by-side comparison | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / apo structure | ||||||
| Function / homology | Function and homology informationtubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / microtubule depolymerization / 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 / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() ![]() ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Wang, Y.X. / Naismith, J.H. / Zhu, X. | ||||||
Citation | Journal: Nat Commun / Year: 2016Title: Pironetin reacts covalently with cysteine-316 of alpha-tubulin to destabilize microtubule Authors: Yang, J. / Wang, Y.X. / Wang, T. / Jiang, J. / Botting, C.H. / Liu, H. / Chen, Q. / Yang, J. / Naismith, J.H. / Zhu, X. / Chen, L. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5jqg.cif.gz | 882.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5jqg.ent.gz | 728 KB | Display | PDB format |
| PDBx/mmJSON format | 5jqg.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/5jqg ftp://data.pdbj.org/pub/pdb/validation_reports/jq/5jqg | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 5fnvC ![]() 4i55S C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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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 natural source / Source: (natural) ![]() #2: Protein | Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #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.) ![]() ![]() #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, 348 molecules 














| #5: Chemical | | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-GDP / | #10: Chemical | #11: Chemical | ChemComp-ACP / | #12: 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: 2.87 Å3/Da / Density % sol: 57.13 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.7 Details: 0.1M MES, 6% PEG4000, 5% Glycerol, 30mM CaCl2, 30mM MgCl2 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
| Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2014 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
| Reflection | Resolution: 2.24→35.22 Å / Num. obs: 144729 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 14.9 |
| Reflection shell | Resolution: 2.24→2.3 Å |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 4I55 Resolution: 2.24→35.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.577 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 49.326 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.24→35.22 Å
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| Refine LS restraints |
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