+Open data
-Basic information
Entry | Database: PDB / ID: 3kud | ||||||
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Title | Complex of Ras-GDP with RafRBD(A85K) | ||||||
Components |
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Keywords | GTP BINDING PROTEIN/TRANSFERASE / Ras-effector complex / GTP-binding / Nucleotide-binding / Proto-oncogene / Transferase / GTP BINDING PROTEIN-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 / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / positive regulation of wound healing / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / defense response to protozoan / face development / pseudopodium / somatic stem cell population maintenance / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / 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 / : / 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 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / 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 / activation of adenylate cyclase activity / EGFR Transactivation by Gastrin / response to muscle stretch / myelination / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / small monomeric GTPase / insulin-like growth factor receptor signaling pathway / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / thymus development / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / Signaling by ERBB2 TMD/JMD mutants / positive regulation of JNK cascade Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Filchtinski, D. / Sharabi, O. / Rueppel, A. / Vetter, I.R. / Herrmann, C. / Shifman, J.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: What makes Ras an efficient molecular switch: a computational, biophysical, and structural study of Ras-GDP interactions with mutants of Raf. Authors: Filchtinski, D. / Sharabi, O. / Ruppel, A. / Vetter, I.R. / Herrmann, C. / Shifman, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kud.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kud.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/3kud ftp://data.pdbj.org/pub/pdb/validation_reports/ku/3kud | HTTPS FTP |
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-Related structure data
Related structure data | 3kucC 1guaS 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: 18875.191 Da / Num. of mol.: 1 / Fragment: UNP residues 1-166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112 |
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#2: Protein | Mass: 9261.867 Da / Num. of mol.: 1 / Fragment: UNP residues 51-131 / Mutation: A85K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Production host: Escherichia coli (E. coli) References: UniProt: P04049, non-specific serine/threonine protein kinase |
#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.3M Na-Malonat pH 6.0, 100 mM MES pH 6.1, 4% Betaine, 2% Sarcosine, 2% N,N-dimethylglycine, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97935 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2004 |
Radiation | Monochromator: FOCUSED SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. all: 24673 / Num. obs: 24583 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.83 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.052 / Net I/σ(I): 14.76 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.83 / Num. unique all: 1473 / Rsym value: 0.379 / % possible all: 82.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1gua Resolution: 2.15→19.68 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.576 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.169 / 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: 39.254 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→19.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.205 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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