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Yorodumi- PDB-3cu8: Impaired binding of 14-3-3 to Raf1 is linked to Noonan and LEOPAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cu8 | ||||||
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Title | Impaired binding of 14-3-3 to Raf1 is linked to Noonan and LEOPARD syndrome | ||||||
Components |
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Keywords | PROTEIN BINDING / SIGNALING PROTEIN / 14-3-3 / zeta / adapter protein / cRaf1 / NOONAN syndrome / LEOPARD syndrome / Phosphoprotein | ||||||
Function / homology | Function and homology information death-inducing signaling complex assembly / Golgi reassembly / intermediate filament cytoskeleton organization / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling ...death-inducing signaling complex assembly / Golgi reassembly / intermediate filament cytoskeleton organization / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / insulin secretion involved in cellular response to glucose stimulus / negative regulation of protein localization to nucleus / Negative feedback regulation of MAPK pathway / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / face development / pseudopodium / somatic stem cell population maintenance / neurotrophin TRK receptor signaling pathway / thyroid gland development / Regulation of localization of FOXO transcription factors / extrinsic apoptotic signaling pathway via death domain receptors / Interleukin-3, Interleukin-5 and GM-CSF signaling / MAP kinase kinase kinase activity / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / negative regulation of protein-containing complex assembly / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Schwann cell development / type II interferon-mediated signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / response to muscle stretch / activation of adenylate cyclase activity / myelination / CD209 (DC-SIGN) signaling / negative regulation of innate immune response / protein sequestering activity / regulation of ERK1 and ERK2 cascade / insulin-like growth factor receptor signaling pathway / thymus development / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / wound healing / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / MAP2K and MAPK activation / Stimuli-sensing channels / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / melanosome / MAPK cascade / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / blood microparticle / regulation of apoptotic process / DNA-binding transcription factor binding / vesicle / mitochondrial outer membrane / transmembrane transporter binding / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / negative regulation of cell population proliferation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / RNA binding / extracellular exosome / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Schumacher, B. / Weyand, M. / Kuhlmann, J. / Ottmann, C. | ||||||
Citation | Journal: Mol. Cell. Biol. / Year: 2010 Title: Impaired binding of 14-3-3 to C-RAF in Noonan syndrome suggests new approaches in diseases with increased Ras signaling. Authors: Molzan, M. / Schumacher, B. / Ottmann, C. / Baljuls, A. / Polzien, L. / Weyand, M. / Thiel, P. / Rose, R. / Rose, M. / Kuhenne, P. / Kaiser, M. / Rapp, U.R. / Kuhlmann, J. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cu8.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cu8.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 3cu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/3cu8 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/3cu8 | HTTPS FTP |
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-Related 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: 27777.092 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P63104 #2: Protein/peptide | Mass: 1080.046 Da / Num. of mol.: 2 / Fragment: Phosphorylated cRaf1 peptide / Source method: obtained synthetically Details: Raf1pSer259 peptide (NH2-255QRSTpSTPNVHA265-COOH) was synthesized by Biosyntan (Berlin, Germany). Source: (synth.) Homo sapiens (human) References: UniProt: P04049, non-specific serine/threonine protein kinase #3: Chemical | #4: Chemical | ChemComp-PPI / | #5: 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: 2.94 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M (Sodium propionate, sodium cacodylate, BIS-TRIS propane), 27% PEG 1500, 2mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97809 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2007 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator, Sagittal-horizontal; Dynamically bendable mirror, Meridional-vertical Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97809 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. all: 27180 / Num. obs: 27180 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.95 % / Rmerge(I) obs: 0.052 / Rsym value: 0.2044 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 5 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 4.02 / Num. unique all: 3084 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.344 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.642 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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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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