+Open data
-Basic information
Entry | Database: PDB / ID: 5air | ||||||
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Title | Structural analysis of mouse GSK3beta fused with LRP6 peptide. | ||||||
Components | Low-density lipoprotein receptor-related protein 6,Glycogen synthase kinase-3 beta | ||||||
Keywords | TRANSFERASE / LRP6 / GSK3 BETA | ||||||
Function / homology | Function and homology information hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuron maturation / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / Beta-catenin phosphorylation cascade / Wnt signaling pathway involved in somitogenesis / CRMPs in Sema3A signaling ...hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuron maturation / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / Beta-catenin phosphorylation cascade / Wnt signaling pathway involved in somitogenesis / CRMPs in Sema3A signaling / membrane-bounded organelle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of synaptic assembly at neuromuscular junction / myotube differentiation / positive regulation of osteoclast proliferation / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / negative regulation of neuron migration / neural crest formation / cell growth involved in cardiac muscle cell development / receptor-mediated endocytosis involved in cholesterol transport / positive regulation of cardiac muscle cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of dendrite morphogenesis / Degradation of beta-catenin by the destruction complex / kinase inhibitor activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of cardiac muscle hypertrophy / positive regulation of stem cell differentiation / toxin transmembrane transporter activity / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / protein localization to microtubule / negative regulation of dendrite development / superior temporal gyrus development / positive regulation of protein localization to cilium / GLI3 is processed to GLI3R by the proteasome / Wnt-protein binding / cellular response to cholesterol / negative regulation of dopaminergic neuron differentiation / midbrain dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / autosome genomic imprinting / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / meiosis I / positive regulation of cilium assembly / bone remodeling / myoblast fusion / negative regulation of protein acetylation / negative regulation of protein serine/threonine kinase activity / negative regulation of TOR signaling / protein serine/threonine kinase binding / beta-catenin destruction complex / tau-protein kinase / dopaminergic neuron differentiation / regulation of microtubule-based process / regulation of modification of postsynaptic structure / regulation of protein export from nucleus / frizzled binding / positive regulation of osteoclast differentiation / axon extension / neural crest cell differentiation / cellular response to interleukin-3 / regulation of axon extension / Wnt signalosome / cellular response to glucocorticoid stimulus / regulation of long-term synaptic potentiation / positive regulation of mitochondrial membrane potential / meiotic spindle / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / regulation of osteoblast differentiation / establishment or maintenance of cell polarity / positive regulation of DNA biosynthetic process / dynein complex binding / cellular response to hepatocyte growth factor stimulus / regulation of neuronal synaptic plasticity / regulation of dendrite morphogenesis / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / response to zinc ion / glycogen metabolic process / ER overload response / regulation of neuron projection development / fat cell differentiation / hepatocyte apoptotic process / positive regulation of osteoblast proliferation / negative regulation of smooth muscle cell apoptotic process / dynactin binding / protein kinase A catalytic subunit binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.53 Å | ||||||
Authors | Kim, K.L. | ||||||
Citation | Journal: Biodesign / Year: 2015 Title: Structural Analysis of Mouse Gsk3 Beta Fused with Lrp6 Peptide Authors: Kim, K.L. / Kim, J.S. / Cha, J.S. / Cho, H.S. / Ha, N.C. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5air.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5air.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 5air.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/5air ftp://data.pdbj.org/pub/pdb/validation_reports/ai/5air | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47822.422 Da / Num. of mol.: 2 Fragment: RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420 Source method: isolated from a genetically manipulated source Details: ac-to-Bac baculovirus expression system,ac-to-Bac baculovirus expression system Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse) Gene: LRP6, Gsk3b / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O75581, UniProt: Q9WV60, tau-protein kinase, non-specific serine/threonine protein kinase #2: Chemical | #3: 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: 3.3 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200 MM SODIUM MALONATE, 20 % (V/V) PEG 3350, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→177.5 Å / Num. obs: 42941 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.37 |
-Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 2.53→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.218 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 49.199 Å2
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Refinement step | Cycle: LAST / Resolution: 2.53→20 Å
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