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Yorodumi- PDB-1bwn: PH DOMAIN AND BTK MOTIF FROM BRUTON'S TYROSINE KINASE MUTANT E41K... -
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-Basic information
Entry | Database: PDB / ID: 1bwn | ||||||
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Title | PH DOMAIN AND BTK MOTIF FROM BRUTON'S TYROSINE KINASE MUTANT E41K IN COMPLEX WITH INS(1,3,4,5)P4 | ||||||
Components | BRUTON'S TYROSINE KINASE | ||||||
Keywords | TRANSFERASE / PH DOMAIN / BTK MOTIF / INOSITOL-(1 / 3 / 4 / 5)-TETRAKISPHOSPHATE / ZINC BINDING / X-LINKED AGAMMAGLOBULINEMIA / TYROSINE-PROTEIN KINASE | ||||||
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 / histamine secretion by mast cell / positive regulation of synoviocyte proliferation ...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 / histamine secretion by mast cell / positive regulation of synoviocyte proliferation / 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) / 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 / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / mesoderm development / positive regulation of immunoglobulin production / RHO GTPases Activate WASPs and WAVEs / positive regulation of phagocytosis / positive regulation of B cell proliferation / cell maturation / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium-mediated signaling / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G beta:gamma signalling through BTK / Regulation of actin dynamics for phagocytic cup formation / cellular response to reactive oxygen species / positive regulation of interleukin-6 production / peptidyl-tyrosine phosphorylation / G alpha (12/13) signalling events / positive regulation of tumor necrosis factor production / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / T cell receptor signaling pathway / cytoplasmic vesicle / G alpha (q) signalling events / protein tyrosine kinase activity / Potential therapeutics for SARS / response to lipopolysaccharide / adaptive immune response / intracellular signal transduction / membrane raft / protein phosphorylation / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Djinovic Carugo, K. / Baraldi, E. / Hyvoenen, M. / Lo Surdo, P. / Riley, A. / Potter, B. / Saraste, M. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Structure of the PH domain from Bruton's tyrosine kinase in complex with inositol 1,3,4,5-tetrakisphosphate. Authors: Baraldi, E. / Carugo, K.D. / Hyvonen, M. / Surdo, P.L. / Riley, A.M. / Potter, B.V. / O'Brien, R. / Ladbury, J.E. / Saraste, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bwn.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bwn.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bwn ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bwn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.331013, 0.942566, -0.044724), Vector: |
-Components
#1: Protein | Mass: 19983.078 Da / Num. of mol.: 2 / Fragment: PH DOMAIN AND BTK MOTIF / Mutation: E41K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: BL21 / Plasmid: PBAT4-BTK3E41K / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q06187, EC: 2.7.1.112 #2: Chemical | #3: Chemical | ChemComp-4IP / #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: 4.12 Å3/Da / Density % sol: 70.1 % | ||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | ||||||||||||||||||||
Crystal grow | *PLUS 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: ID14-3 / Wavelength: 0.947 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.947 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35 Å / Num. obs: 39294 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 37.9 Å2 / Rsym value: 0.037 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rsym value: 0.322 / % possible all: 99.5 |
Reflection | *PLUS Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.322 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BWN Resolution: 2.1→35 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: MOEWS AND KRETSINGER (J.MOL.BIOL. (1975), 91, 201-228) Bsol: 262.7 Å2 / ksol: 0.844 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→35 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5EB / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.214 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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