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Yorodumi- PDB-5zc6: Solution structure of H-RasT35S mutant protein in complex with KBFM123 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zc6 | |||||||||
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Title | Solution structure of H-RasT35S mutant protein in complex with KBFM123 | |||||||||
Components | GTPase HRas | |||||||||
Keywords | ONCOPROTEIN / Inhibitor / Complex / Cancer / Small GTPases | |||||||||
Function / homology | Function and homology information GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / myelination / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of epithelial cell proliferation / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / positive regulation of MAP kinase activity / regulation of long-term neuronal synaptic plasticity / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / endocytosis / positive regulation of type II interferon production / 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 / GDP binding / chemotaxis / MAPK cascade / cellular senescence / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / DAP12 signaling Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Matsumoto, S. / Hayashi, Y. / Hiraga, T. / Matsuo, K. / Kataoka, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Biochemistry / Year: 2018 Title: Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring Authors: Matsumoto, S. / Hiraga, T. / Hayashi, Y. / Yoshikawa, Y. / Tsuda, C. / Araki, M. / Neya, M. / Shima, F. / Kataoka, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zc6.cif.gz | 800.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zc6.ent.gz | 659.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/5zc6 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/5zc6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18861.166 Da / Num. of mol.: 1 / Fragment: UNP residues 1-166 / Mutation: T35S 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: Chemical | ChemComp-GNP / |
#3: Chemical | ChemComp-KBF / |
#4: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.8 mM [U-99% 13C; U-99% 15N] H-RasT35S, 3.0 mM KBFM123, 20 mM sodium phosphate, 40 mM sodium chloride, 8 mM MAGNESIUM ION, 0.8 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, 80% D2O/20% d6-DMSO Label: sample_1 / Solvent system: 80% D2O/20% d6-DMSO | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 mM / Label: conditions_1 / pH: 6.8 / Pressure: ambient Pa / Temperature: 278 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software | Name: CNS / Developer: BRUNGER A. T. ET.AL. / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 15 |