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Yorodumi- PDB-1mwn: Solution NMR structure of S100B bound to the high-affinity target... -
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-Basic information
Entry | Database: PDB / ID: 1mwn | ||||||
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Title | Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / S100B / TRTK-12 / Calcium-binding / EF-hand / S100 protein / four helix bundle / helix loop helix / protein-peptide complex / 20 structures | ||||||
Function / homology | Function and homology information negative regulation of skeletal muscle cell differentiation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / TAK1-dependent IKK and NF-kappa-B activation / WASH complex / F-actin capping protein complex / adaptive thermogenesis / sympathetic neuron projection extension / positive regulation of myelination / RAGE receptor binding ...negative regulation of skeletal muscle cell differentiation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / TAK1-dependent IKK and NF-kappa-B activation / WASH complex / F-actin capping protein complex / adaptive thermogenesis / sympathetic neuron projection extension / positive regulation of myelination / RAGE receptor binding / COPI-independent Golgi-to-ER retrograde traffic / cell junction assembly / barbed-end actin filament capping / response to methylmercury / ion binding / astrocyte differentiation / S100 protein binding / Sensory processing of sound by inner hair cells of the cochlea / neuron projection extension / regulation of neuronal synaptic plasticity / Advanced glycosylation endproduct receptor signaling / positive regulation of synaptic transmission / COPI-mediated anterograde transport / response to glucocorticoid / ruffle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / positive regulation of neuron differentiation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcoplasmic reticulum / long-term synaptic potentiation / tau protein binding / memory / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / actin binding / Factors involved in megakaryocyte development and platelet production / regulation of cell shape / cellular response to hypoxia / actin cytoskeleton organization / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cytoskeleton / cell adhesion / cadherin binding / positive regulation of apoptotic process / signaling receptor binding / neuronal cell body / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Inman, K.G. / Yang, R. / Rustandi, R.R. / Miller, K.E. / Baldisseri, D.M. / Weber, D.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12 Authors: Inman, K.G. / Yang, R. / Rustandi, R.R. / Miller, K.E. / Baldisseri, D.M. / Weber, D.J. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: Structure of the negative regulatory domain of p53 bound to S100B(betabeta) Authors: Rustandi, R.R. / Baldisseri, D.M. / Weber, D.J. #2: Journal: Biochemistry / Year: 1998 Title: Solution structure of calcium-bound rat S100B(betabeta) as determined by nuclear magnetic resonance spectroscopy Authors: Drohat, A.C. / Baldisseri, D.M. / Rustandi, R.R. / Weber, D.J. #3: Journal: Biochemistry / Year: 1996 Title: Solution structure of rat apo-S100B(betabeta) as determined by NMR spectroscopy Authors: Drohat, A.C. / Amburgey, J.C. / Abildgaard, F. / Starich, M.R. / Baldisseri, D.M. / Weber, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mwn.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1mwn.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1mwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/1mwn ftp://data.pdbj.org/pub/pdb/validation_reports/mw/1mwn | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 10758.048 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100B / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) / References: UniProt: P04631 #2: Protein/peptide | Mass: 1477.728 Da / Num. of mol.: 2 / Fragment: Residues 265-276 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: P52907 #3: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 2.2 mM S100B (subunit concentration), 5.2 mM CaCl2, 2.6 mM TRTK-12 peptide, 10 mM tris-d11, 15 mM NaCl, 0.1 mM EDTA, 5 mM DTT, 0.35 mM NaN3 Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 25 mM / pH: 6.5 / Pressure: ambient / Temperature: 310 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing / Software ordinal: 1 | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |