+Open data
-Basic information
Entry | Database: PDB / ID: 4o27 | ||||||
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Title | Crystal structure of MST3-MO25 complex with WIF motif | ||||||
Components |
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Keywords | TRANSFERASE ACTIVATOR/TRANSFERASE / Scaffold protein / Protein Ser/Thr kinase / TRANSFERASE ACTIVATOR-TRANSFERASE complex / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / Apoptotic execution phase / serine/threonine protein kinase complex / cellular hypotonic response / regulation of axon regeneration / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress ...negative regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / Apoptotic execution phase / serine/threonine protein kinase complex / cellular hypotonic response / regulation of axon regeneration / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / protein kinase activator activity / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / protein serine/threonine kinase activator activity / negative regulation of cell migration / positive regulation of peptidyl-threonine phosphorylation / response to activity / positive regulation of protein serine/threonine kinase activity / response to hydrogen peroxide / kinase binding / Z disc / peptidyl-serine phosphorylation / secretory granule lumen / ficolin-1-rich granule lumen / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cadherin binding / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.185 Å | ||||||
Authors | Hao, Q. / Feng, M. / Zhou, Z.C. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2014 Title: Structural insights into regulatory mechanisms of MO25-mediated kinase activation. Authors: Hao, Q. / Feng, M. / Shi, Z. / Li, C. / Chen, M. / Wang, W. / Zhang, M. / Jiao, S. / Zhou, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o27.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o27.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 4o27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/4o27 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/4o27 | HTTPS FTP |
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-Related structure data
Related structure data | 4nzwC 1uplS 3a7jS 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
#1: Protein | Mass: 38053.785 Da / Num. of mol.: 1 / Fragment: Mo25-like, UNP residues 11-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAB39, CGI-66, MO25 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y376 |
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#2: Protein | Mass: 31965.729 Da / Num. of mol.: 1 / Fragment: Kinase domain, UNP residues 30-309 / Mutation: T190E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MST3, STK24, STK3 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase |
#3: Protein/peptide | Mass: 708.758 Da / Num. of mol.: 1 / Fragment: WIF motif, UNP residues 336-340 / Mutation: T340E / Source method: obtained synthetically / Details: The peptide was chemically synthesized. References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase |
#4: Chemical | ChemComp-ADP / |
#5: Chemical | ChemComp-MN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 2.0M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-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: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.185→50 Å / Num. all: 18586 / Num. obs: 18586 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 4.84 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A7J, 1UPL Resolution: 3.185→46.55 Å / SU ML: 0.44 / σ(F): 1.35 / Phase error: 27.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.185→46.55 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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