+Open data
-Basic information
Entry | Database: PDB / ID: 5csi | ||||||
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Title | S100B-RSK1 crystal structure A' | ||||||
Components |
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Keywords | TRANSFERASE / Kinase / Signaling / Inhibitor / S100 | ||||||
Function / homology | Function and homology information regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / adaptive thermogenesis / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / sympathetic neuron projection extension / RAGE receptor binding / Gastrin-CREB signalling pathway via PKC and MAPK ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / adaptive thermogenesis / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / sympathetic neuron projection extension / RAGE receptor binding / Gastrin-CREB signalling pathway via PKC and MAPK / ion binding / RSK activation / S100 protein binding / negative regulation of TOR signaling / regulation of neuronal synaptic plasticity / ERK/MAPK targets / Recycling pathway of L1 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation / protein serine/threonine/tyrosine kinase activity / axonogenesis / sarcoplasmic reticulum / central nervous system development / positive regulation of cell differentiation / TAK1-dependent IKK and NF-kappa-B activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / tau protein binding / memory / calcium-dependent protein binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / chemical synaptic transmission / positive regulation of canonical NF-kappaB signal transduction / learning or memory / non-specific serine/threonine protein kinase / cell adhesion / intracellular signal transduction / cell cycle / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / synapse / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / magnesium ion binding / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / zinc ion binding / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Gogl, G. / Nyitray, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Basis of Ribosomal S6 Kinase 1 (RSK1) Inhibition by S100B Protein: MODULATION OF THE EXTRACELLULAR SIGNAL-REGULATED KINASE (ERK) SIGNALING CASCADE IN A CALCIUM-DEPENDENT WAY. Authors: Gogl, G. / Alexa, A. / Kiss, B. / Katona, G. / Kovacs, M. / Bodor, A. / Remenyi, A. / Nyitray, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5csi.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5csi.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 5csi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/5csi ftp://data.pdbj.org/pub/pdb/validation_reports/cs/5csi | HTTPS FTP |
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-Related structure data
Related structure data | 5csfC 5csjC 5csnC 3cztS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11009.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S100B / Production host: Escherichia coli (E. coli) / References: UniProt: P04271 #2: Protein/peptide | | Mass: 5260.097 Da / Num. of mol.: 1 / Fragment: UNP residues 689-735 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA1, MAPKAPK1A, RSK1 / Production host: Escherichia coli (E. coli) References: UniProt: Q15418, non-specific serine/threonine protein kinase #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.62 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes 7, 150 mM NaCl, 20% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→37.65 Å / Num. obs: 15160 / % possible obs: 99.9 % / Redundancy: 6.43 % / Rsym value: 0.055 / Net I/σ(I): 18.77 |
Reflection shell | Resolution: 2.13→2.19 Å / Redundancy: 6.73 % / Mean I/σ(I) obs: 2.07 / Rsym value: 0.828 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CZT Resolution: 2.13→37.65 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→37.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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