+Open data
-Basic information
Entry | Database: PDB / ID: 4zhq | ||||||
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Title | Crystal structure of Tubulin-Stathmin-TTL-MMAE Complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/INHIBITOR / STRUCTURAL PROTEIN-INHIBITOR Complex | ||||||
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 / 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 | Rattus norvegicus (Norway rat) Gallus gallus (chicken) Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Wang, Y. / Zhang, R. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2016 Title: Structural Insights into the Pharmacophore of Vinca Domain Inhibitors of Microtubules Authors: Wang, Y. / Benz, F.W. / Wu, Y. / Wang, Q. / Chen, Y. / Chen, X. / Li, H. / Zhang, Y. / Zhang, R. / Yang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zhq.cif.gz | 464.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zhq.ent.gz | 368.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/4zhq ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zhq | HTTPS FTP |
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-Related structure data
Related structure data | 4zi7C 4zolC 5bmvC 4tv8S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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 natural source / Source: (natural) Sus scrofa (pig) / Organ: BRAIN / References: UniProt: Q2XVP4 #2: Protein | Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: BRAIN / References: UniProt: P02554 #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, 320 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-GOL / #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-4Q5 / | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 717.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H67N5O7 References: N-methyl-L-valyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide Comment: antineoplastic*YM #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: 2.87 Å3/Da / Density % sol: 57.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.7 Details: 6% PEG, 5% glycerol, 0.1M MES, 30 mM CaCl2, 30 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→39.34 Å / Num. obs: 98202 / % possible obs: 99.7 % / Redundancy: 7.4 % / Net I/σ(I): 13.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TV8 Resolution: 2.55→39.34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 43.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→39.34 Å
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LS refinement shell | Resolution: 2.55→2.62 Å / Total num. of bins used: 20
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