+Open data
-Basic information
Entry | Database: PDB / ID: 2z0p | ||||||
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Title | Crystal structure of PH domain of Bruton's tyrosine kinase | ||||||
Components | Tyrosine-protein kinase BTK | ||||||
Keywords | SIGNALING PROTEIN / PH domain / PIP3C4 / ATP-binding / Disease mutation / Kinase / Membrane / Metal-binding / Nucleotide-binding / Nucleus / Phosphorylation / SH2 domain / SH3 domain / Transferase / Tyrosine-protein kinase / Zinc-finger / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell ...regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / cellular response to interleukin-7 / MyD88 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of immunoglobulin production / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of interleukin-10 production / B cell activation / negative regulation of B cell proliferation / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / cell maturation / RHO GTPases Activate WASPs and WAVEs / positive regulation of B cell proliferation / positive regulation of phagocytosis / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / calcium-mediated signaling / non-membrane spanning protein tyrosine kinase activity / cellular response to reactive oxygen species / peptidyl-tyrosine phosphorylation / Regulation of actin dynamics for phagocytic cup formation / G beta:gamma signalling through BTK / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / G alpha (12/13) signalling events / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / protein tyrosine kinase activity / cytoplasmic vesicle / Potential therapeutics for SARS / G alpha (q) signalling events / adaptive immune response / response to lipopolysaccharide / intracellular signal transduction / membrane raft / protein phosphorylation / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Mishima, C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 Title: Crystal structure of the Bruton's tyrosine kinase PH domain with phosphatidylinositol Authors: Murayama, K. / Kato-Murayama, M. / Mishima, C. / Akasaka, R. / Shirouzu, M. / Fukui, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z0p.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z0p.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 2z0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z0p_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2z0p_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2z0p_validation.xml.gz | 30 KB | Display | |
Data in CIF | 2z0p_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/2z0p ftp://data.pdbj.org/pub/pdb/validation_reports/z0/2z0p | HTTPS FTP |
-Related structure data
Related structure data | 1btkS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19983.014 Da / Num. of mol.: 4 / Fragment: PH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q06187, non-specific protein-tyrosine kinase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-4PT / ( #4: 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: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG3350, 0.2M Li2SO4, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→29.67 Å / Num. obs: 26621 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.037 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.58→2.67 Å / Rsym value: 0.114 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BTK Resolution: 2.58→29.67 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1076225.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.8175 Å2 / ksol: 0.353675 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.58→29.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.58→2.74 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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