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- PDB-8jog: solution structure of Ras Binding Domein (RBD) in C-RAF with nega... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jog | |||||||||
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Title | solution structure of Ras Binding Domein (RBD) in C-RAF with negative allosteric modulator. | |||||||||
![]() | RAF proto-oncogene serine/threonine-protein kinase | |||||||||
![]() | SIGNALING PROTEIN / MAPK | |||||||||
Function / homology | ![]() death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / 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 feedback regulation of MAPK pathway ...death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / 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 feedback regulation of MAPK pathway / 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 / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / negative regulation of protein-containing complex assembly / Schwann cell development / type II interferon-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / activation of adenylate cyclase activity / response to muscle stretch / myelination / CD209 (DC-SIGN) signaling / insulin-like growth factor receptor signaling pathway / thymus development / RAF activation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / 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 / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / regulation of apoptotic process / mitochondrial outer membrane / Ras protein signal transduction / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
![]() | Makino, Y. / Matsumoto, S. / Yoshikawa, Y. / Kawamura, T. / Kumasaka, T. / Shima, F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers Authors: Yoshikawa, Y. / Makino, Y. / Kubota, H. / Kawamura, T. / Matsumoto, S. / Yuki, H. / Shibaike, A. / Okamura, M. / Okada, T. / Kataoka, T. / Honma, T. / Kumasaka, T. / Koyama, H. / Shima, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 614.4 KB | Display | ![]() |
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PDB format | ![]() | 520.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.7 KB | Display | ![]() |
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Full document | ![]() | 647.3 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 56 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jnaC ![]() 8jnbC ![]() 8jofC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 9615.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04049, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 0.3 mM [U-100% 13C; U-100% 15N] Serin/threonine protein kinase C-RAF, 25 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium dichloride, 90% H2O/10% D2O Label: 13C/15N_sample / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 85 mM / Label: condition_1 / pH: 6.8 / Pressure: ambient atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: cryo-probe |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 | ||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: 20 / Conformers calculated total number: 20 / Conformers submitted total number: 20 |