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Yorodumi- PDB-1awx: SH3 DOMAIN FROM BRUTON'S TYROSINE KINASE, NMR, MINIMIZED AVERAGE ... -
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-Basic information
Entry | Database: PDB / ID: 1awx | ||||||
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Title | SH3 DOMAIN FROM BRUTON'S TYROSINE KINASE, NMR, MINIMIZED AVERAGE STRUCTURE | ||||||
Components | BRUTON'S TYROSINE KINASE | ||||||
Keywords | TRANSFERASE / TYROSINE KINASE / X-LINKED AGAMMAGLOBULINEMIA / XLA / BTK / SH3 DOMAIN | ||||||
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 | SOLUTION NMR / AB INITIO - SIMULATED ANNEALING | ||||||
Authors | Hansson, H. / Mattsson, P.T. / Allard, P. / Haapaniemi, P. / Vihinen, M. / Smith, C.I.E. / Hard, T. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Solution structure of the SH3 domain from Bruton's tyrosine kinase. Authors: Hansson, H. / Mattsson, P.T. / Allard, P. / Haapaniemi, P. / Vihinen, M. / Smith, C.I. / Hard, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1awx.cif.gz | 30.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1awx.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 1awx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/1awx ftp://data.pdbj.org/pub/pdb/validation_reports/aw/1awx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7772.562 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: PGEX-4T-3 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q06187, EC: 2.7.1.112 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 6.5 / Temperature: 303 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian UNITY 500 / Manufacturer: Varian / Model: UNITY 500 / Field strength: 500 MHz |
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-Processing
Software |
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NMR software |
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Refinement | Method: AB INITIO - SIMULATED ANNEALING / Software ordinal: 1 Details: THE STRUCTURE WAS DETERMINED USING 756 DISTANCE RESTRAINTS, 52 DIHEDRAL ANGLE RESTRAINTS AND 22 HYDROGEN BOND RESTRAINTS. THE HYDROGEN BOND RESTRAINTS WERE USED ONLY IN THE LAST STEP OF ...Details: THE STRUCTURE WAS DETERMINED USING 756 DISTANCE RESTRAINTS, 52 DIHEDRAL ANGLE RESTRAINTS AND 22 HYDROGEN BOND RESTRAINTS. THE HYDROGEN BOND RESTRAINTS WERE USED ONLY IN THE LAST STEP OF REFINEMENT. 50 STRUCTURES WERE CALCULATED AND REFINED USING AB INITIO SIMULATED ANNEALING PROTOCOL FOR X-PLOR (1). ALL FORCE CONSTANTS AND POTENTIALS WERE SET TO THE DEFAULT (PROTOCOL) VALUES EXCEPT FOR THE VAN DER WAALS' RADII SCALE FACTOR ("REPEL"), WHICH WAS DECREASED TO 0.80 INSTEAD OF 0.75 DURING THE FINAL COOLING STAGES IN THE REFINEMENT. THIS RESULTS IN MORE REASONABLE BACKBONE CONFORMATION AND SOMEWHAT HIGHER X-PLOR TOTAL ENERGIES. CENTER AVERAGING PSEUDOATOM CORRECTION WAS USED FOR ALL DISTANCE RESTRAINT S(2). ON THE BASIS OF X-PLOR TOTAL ENERGY 42 LOWEST ENERGY STRUCTURES WERE SELECTED. THE AVERAGE AND MINIMIZED STRUCTURE WAS CALCULATED BY AVERAGING SUPERIMPOSED STRUCTURES IN THE ENSEMBLE AND THEN ENERGY MINIMIZING THE AVERAGE STRUCTURE. THE POTENTIALS AND CONSTANTS USED IN THE ENERGY MINIMIZATION WERE THE SAME FOR THE AVERAGE STRUCTURE AND THE ENSEMBLE STRUCTURES. | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: MINIMIZED AVERAGE STRUCTURE BASED ON 42 LOWEST ENERGY STRUCTURES Conformers calculated total number: 50 / Conformers submitted total number: 1 |