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- PDB-4ihl: Human 14-3-3 isoform zeta in complex with a diphoyphorylated C-RA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ihl | ||||||
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Title | Human 14-3-3 isoform zeta in complex with a diphoyphorylated C-RAF peptide and Cotylenin A | ||||||
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![]() | PEPTIDE BINDING PROTEIN / 14-3-3 FOLD / RAF / ALL ALPHA-HELICAL / ADAPTER PROTEIN / PROTEIN-PROTEIN INTERACTION | ||||||
Function / homology | ![]() death-inducing signaling complex assembly / Golgi reassembly / synaptic target recognition / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / regulation of synapse maturation / intermediate filament cytoskeleton organization / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction ...death-inducing signaling complex assembly / Golgi reassembly / synaptic target recognition / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / regulation of synapse maturation / intermediate filament cytoskeleton organization / establishment of Golgi localization / type B pancreatic cell proliferation / 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 / Negative feedback regulation of MAPK pathway / KSRP (KHSRP) binds and destabilizes mRNA / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / 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 / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / phosphoserine residue binding / MAP kinase kinase kinase activity / 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 / cellular response to glucose starvation / 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 / protein sequestering activity / activation of adenylate cyclase activity / response to muscle stretch / ERK1 and ERK2 cascade / myelination / negative regulation of innate immune response / CD209 (DC-SIGN) signaling / hippocampal mossy fiber to CA3 synapse / regulation of ERK1 and ERK2 cascade / insulin-like growth factor receptor signaling pathway / thymus development / Deactivation of the beta-catenin transactivating complex / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / lung development / wound healing / MAP2K and MAPK activation / regulation of protein stability / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / MAPK cascade / Signaling by BRAF and RAF1 fusions / melanosome / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / regulation of apoptotic process / angiogenesis / DNA-binding transcription factor binding / vesicle / mitochondrial outer membrane / transmembrane transporter binding / Ras protein signal transduction / positive regulation of MAPK cascade / blood microparticle / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / negative regulation of cell population proliferation / protein domain specific binding / 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 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Molzan, M. / Ottmann, C. | ||||||
![]() | ![]() Title: Stabilization of Physical RAF/14-3-3 Interaction by Cotylenin A as Treatment Strategy for RAS Mutant Cancers. Authors: Molzan, M. / Kasper, S. / Roglin, L. / Skwarczynska, M. / Sassa, T. / Inoue, T. / Breitenbuecher, F. / Ohkanda, J. / Kato, N. / Schuler, M. / Ottmann, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.3 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ieaC ![]() 4fj3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26720.217 Da / Num. of mol.: 2 / Fragment: UNP residues 1-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 4184.204 Da / Num. of mol.: 1 / Fragment: UNP residues 229-264 / Source method: obtained synthetically Details: synthetic peptide, The full-lenth C-Raf kinase occurs in homo spaiens Source: (synth.) ![]() References: UniProt: P04049, non-specific serine/threonine protein kinase #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M NA-ACETATE PH 7.0, 0.8 M NAH2PO4 AND 1.2 M K2HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: AL2/AL2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→49.4 Å / Num. all: 43603 / Num. obs: 42870 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.794 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.65 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FJ3 Resolution: 2.2→49.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2455 / WRfactor Rwork: 0.2006 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8288 / SU B: 4.988 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1923 / SU Rfree: 0.1776 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 143.15 Å2 / Biso mean: 50.1522 Å2 / Biso min: 24.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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