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Yorodumi- PDB-4g3x: Crystal Structure of Q61L H-Ras-GppNHp bound to the RBD of Raf Kinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g3x | ||||||
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Title | Crystal Structure of Q61L H-Ras-GppNHp bound to the RBD of Raf Kinase | ||||||
Components |
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Keywords | HYDROLASE/TRANSFERASE / H-Ras / Ras / Raf kinase / Raf / GTPase / allosteric regulation / intrinsic hydrolysis / protein-protein interaction / kinase / GTP binding / HYDROLASE-TRANSFERASE complex | ||||||
Function / homology | Function and homology information 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 / GTPase complex / oncogene-induced cell senescence ...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 / GTPase complex / oncogene-induced cell senescence / insulin secretion involved in cellular response to glucose stimulus / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / Negative feedback regulation of MAPK pathway / T-helper 1 type immune response / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / positive regulation of wound healing / ERBB2-ERBB3 signaling pathway / defense response to protozoan / regulation of cell differentiation / face development / pseudopodium / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / somatic stem cell population maintenance / Activation of RAS in B cells / neurotrophin TRK receptor signaling pathway / thyroid gland development / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of protein-containing complex assembly / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / type II interferon-mediated signaling pathway / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / response to muscle stretch / activation of adenylate cyclase activity / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / intrinsic apoptotic signaling pathway / small monomeric GTPase / G protein activity / insulin-like growth factor receptor signaling pathway / thymus development / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Fetics, S.K. / Kearney, B.M. / Buhrman, G. / Mattos, C. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD. Authors: Fetics, S.K. / Guterres, H. / Kearney, B.M. / Buhrman, G. / Ma, B. / Nussinov, R. / Mattos, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g3x.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g3x.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 4g3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/4g3x ftp://data.pdbj.org/pub/pdb/validation_reports/g3/4g3x | HTTPS FTP |
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-Related structure data
Related structure data | 4g0nC 1guaS 3k8yS C: citing same article (ref.) S: Starting model for refinement |
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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: 18860.221 Da / Num. of mol.: 1 / Mutation: Q61L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112 |
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#2: Protein | Mass: 8789.290 Da / Num. of mol.: 1 / Fragment: UNP residues 55-131 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Plasmid: pET302/NT-His / Production host: Escherichia coli (E. coli) References: UniProt: P04049, non-specific serine/threonine protein kinase |
#3: Chemical | ChemComp-GNP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Protein solution: 10 - 18 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% ...Details: Protein solution: 10 - 18 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% PEG 8000. Drop: 3uL protein, 3uL reservoir , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2011 / Details: crystal |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→32.6 Å / Num. all: 6462 / Num. obs: 6462 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 3K8Y for Chain A and PDB 1GUA for Chain B Resolution: 3.25→32.6 Å / σ(F): 0 / Phase error: 32.62 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.25→32.6 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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