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Yorodumi- PDB-3nkx: Impaired binding of 14-3-3 to Raf1 is linked to Noonan and LEOPAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nkx | ||||||
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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 | ||||||
Function / homology | Function and homology information death-inducing signaling complex assembly / Golgi reassembly / synaptic target recognition / intermediate filament cytoskeleton organization / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of synapse maturation / regulation of Rho protein signal transduction ...death-inducing signaling complex assembly / Golgi reassembly / synaptic target recognition / intermediate filament cytoskeleton organization / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of synapse maturation / regulation of Rho protein signal transduction / tube formation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / negative regulation of protein localization to nucleus / insulin secretion involved in cellular response to glucose stimulus / MAP kinase kinase kinase activity / 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 / thyroid gland development / neurotrophin TRK receptor signaling pathway / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / Activation of BAD and translocation to mitochondria / protein targeting / 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 / regulation of ERK1 and ERK2 cascade / Schwann cell development / type II interferon-mediated signaling pathway / activation of adenylate cyclase activity / cellular response to glucose starvation / 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 / protein sequestering activity / response to muscle stretch / ERK1 and ERK2 cascade / negative regulation of innate immune response / myelination / CD209 (DC-SIGN) signaling / hippocampal mossy fiber to CA3 synapse / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / insulin-like growth factor receptor signaling pathway / lung development / 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 / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / regulation of protein stability / 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 / positive regulation of peptidyl-serine phosphorylation / MAPK cascade / Signaling by BRAF and RAF1 fusions / protein localization / melanosome / insulin receptor signaling pathway / DNA-binding transcription factor binding / angiogenesis / regulation of apoptotic process / vesicle / transmembrane transporter binding / mitochondrial outer membrane / positive regulation of MAPK cascade / blood microparticle / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein domain specific binding / protein phosphorylation / negative regulation of cell population proliferation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ubiquitin protein ligase binding / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Schumacher, B. / Weyand, M. / 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 | 3nkx.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nkx.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nkx_validation.pdf.gz | 466.4 KB | Display | wwPDB validaton report |
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Full document | 3nkx_full_validation.pdf.gz | 475.2 KB | Display | |
Data in XML | 3nkx_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 3nkx_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/3nkx ftp://data.pdbj.org/pub/pdb/validation_reports/nk/3nkx | HTTPS FTP |
-Related structure data
Related structure data | 3cu8C 3iqjC 3iquC 3iqvC 3o8iC 1qjbS 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: 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: 1208.175 Da / Num. of mol.: 2 Fragment: phosphorylated C-Raf peptide, UNP residues 255-264 Source method: obtained synthetically / Details: This sequence occurs naturally in humans. References: UniProt: P04049, non-specific serine/threonine protein kinase #3: Chemical | ChemComp-PPI / | #4: 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: 2.92 Å3/Da / Density % sol: 57.93 % |
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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→60.76 Å / Num. all: 27180 / Num. obs: 27180 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.052 / Rsym value: 0.0495 |
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 Starting model: pdb entry 1QJB Resolution: 2.4→60.76 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.827 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.236 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.024 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→60.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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