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Yorodumi- PDB-1upk: Crystal structure of MO25 in complex with a C-terminal peptide of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1upk | ||||||
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Title | Crystal structure of MO25 in complex with a C-terminal peptide of STRAD | ||||||
Components |
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Keywords | TRANSFERASE / MO25 / STRAD / STE-20 RELATED ADAPTOR / ARMADILLO | ||||||
Function / homology | Function and homology information intracellular protein-containing complex / negative regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / serine/threonine protein kinase complex / cellular hypotonic response / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / G1 to G0 transition / protein kinase activator activity / activation of protein kinase activity ...intracellular protein-containing complex / negative regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / serine/threonine protein kinase complex / cellular hypotonic response / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / G1 to G0 transition / protein kinase activator activity / activation of protein kinase activity / protein export from nucleus / protein serine/threonine kinase activator activity / response to activity / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein serine/threonine kinase activity / Z disc / kinase binding / peptidyl-serine phosphorylation / secretory granule lumen / ficolin-1-rich granule lumen / intracellular signal transduction / Neutrophil degranulation / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.85 Å | ||||||
Authors | Milburn, C.C. / Boudeau, J. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Crystal Structure of Mo25 Alpha in Complex with the C-Terminus of the Pseudo Kinase Ste-20 Related Adaptor (Strad) Authors: Milburn, C.C. / Boudeau, J. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1upk.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1upk.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 1upk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/1upk ftp://data.pdbj.org/pub/pdb/validation_reports/up/1upk | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40344.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6T-1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): B834 / References: UniProt: Q9Y376 |
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#2: Protein/peptide | Mass: 1537.579 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 12 AMINO ACIDS, RESIDUES 1-12 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q7RTN6*PLUS |
#3: Chemical | ChemComp-MES / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: 15% PEG 20000, 0.1 M MES PH 5.0, 3.3% W/V D-GLUCOSE MONOHYDRATE. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979355,0.979333 | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2003 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→25 Å / Num. obs: 36794 / % possible obs: 99.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 41.7 | |||||||||
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.9 / % possible all: 99 | |||||||||
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 25 Å / Redundancy: 8.8 % / Num. measured all: 324698 / Rmerge(I) obs: 0.073 | |||||||||
Reflection shell | *PLUS % possible obs: 99 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.9 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1.85→24.15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1411659.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.314326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→24.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / Num. reflection Rfree: 745 / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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