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Yorodumi- PDB-1bj8: THIRD N-TERMINAL DOMAIN OF GP130, NMR, MINIMIZED AVERAGE STRUCTURE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bj8 | ||||||
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Title | THIRD N-TERMINAL DOMAIN OF GP130, NMR, MINIMIZED AVERAGE STRUCTURE | ||||||
Components | GP130 | ||||||
Keywords | RECEPTOR / SIGNAL TRANSDUCER OF IL-6 TYPE CYTOKINES / THIRD N-TERMINAL DOMAIN / TRANSMEMBRANE / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information interleukin-27 receptor activity / oncostatin-M receptor complex / interleukin-11 receptor activity / interleukin-11 binding / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor complex ...interleukin-27 receptor activity / oncostatin-M receptor complex / interleukin-11 receptor activity / interleukin-11 binding / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of adaptive immune response / positive regulation of acute inflammatory response / positive regulation of astrocyte differentiation / intestinal epithelial cell development / positive regulation of platelet aggregation / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / glycogen metabolic process / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / cytokine binding / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / positive regulation of cardiac muscle hypertrophy / MAPK3 (ERK1) activation / growth factor binding / MAPK1 (ERK2) activation / positive regulation of vascular endothelial growth factor production / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / response to cytokine / cytokine-mediated signaling pathway / scaffold protein binding / negative regulation of neuron apoptotic process / receptor complex / membrane raft / external side of plasma membrane / dendrite / neuronal cell body / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING | ||||||
Authors | Kernebeck, T. / Pflanz, S. / Muller-Newen, G. / Kurapkat, G. / Scheek, R.M. / Dijkstra, K. / Heinrich, P.C. / Wollmer, A. / Grzesiek, S. / Grotzinger, J. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: The signal transducer gp130: solution structure of the carboxy-terminal domain of the cytokine receptor homology region. Authors: Kernebeck, T. / Pflanz, S. / Muller-Newen, G. / Kurapkat, G. / Scheek, R.M. / Dijkstra, K. / Heinrich, P.C. / Wollmer, A. / Grzesiek, S. / Grotzinger, J. #1: Journal: Eur.J.Biochem. / Year: 1997 Title: The Signal Transducer Gp130--Bacterial Expression, Refolding and Properties of the Carboxy-Terminal Domain of the Cytokine-Binding Module Authors: Muller-Newen, G. / Pflanz, S. / Hassiepen, U. / Stahl, J. / Wollmer, A. / Heinrich, P.C. / Grotzinger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bj8.cif.gz | 24.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bj8.ent.gz | 16.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/1bj8 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/1bj8 | 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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NMR ensembles |
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-Components
#1: Protein | Mass: 12652.174 Da / Num. of mol.: 1 / Fragment: THIRD N-TERMINAL DOMAIN / Mutation: V1M, Y2D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40189 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN |
-Sample preparation
Details | Contents: WATER |
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Sample conditions | Ionic strength: 200 mM NACL / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING Software ordinal: 1 Details: THE FINAL 22 STRUCTURES WERE CALCULATED USING A TOTAL OF 1575 RESTRAINTS. DISTANCE BOUND DRIVEN DYNAMICS WAS DONE FOR 1000 STEPS AT 1000 KELVIN, FOLLOWED BY 1000 STEPS OF SIMULATED ANNEALING ...Details: THE FINAL 22 STRUCTURES WERE CALCULATED USING A TOTAL OF 1575 RESTRAINTS. DISTANCE BOUND DRIVEN DYNAMICS WAS DONE FOR 1000 STEPS AT 1000 KELVIN, FOLLOWED BY 1000 STEPS OF SIMULATED ANNEALING TO 10 KELVIN. THE MEAN STRUCTURE WAS ENERGY MINIMIZED USING THE GROMOS PROGRAMM PACKAGE. | |||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 22 / Conformers submitted total number: 1 |