+Open data
-Basic information
Entry | Database: PDB / ID: 3kkm | ||||||
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Title | Crystal structure of H-Ras T35S in complex with GppNHp | ||||||
Components | GTPase HRas | ||||||
Keywords | SIGNALING PROTEIN / GTP-binding / GTPase | ||||||
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 / GRB2 events in EGFR signaling / EGFR Transactivation by Gastrin / SHC1 events in EGFR signaling / positive regulation of protein targeting to membrane / Signalling to RAS / GRB2 events in ERBB2 signaling / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC1 events in ERBB2 signaling / 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 / positive regulation of epithelial cell proliferation / 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 / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / myelination / Signaling by FGFR1 in disease / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / Signaling by ERBB2 TMD/JMD mutants / small monomeric GTPase / positive regulation of MAP kinase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Signaling by SCF-KIT / cellular senescence / cellular response to gamma radiation / positive regulation of fibroblast proliferation / 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 / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Muraoka, S. / Shima, F. / Liao, J. / Ijiri, Y. / Matsumoto, K. / Ye, M. / Inoue, T. / Kataoka, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural basis for conformational dynamics of GTP-bound Ras protein Authors: Shima, F. / Ijiri, Y. / Muraoka, S. / Liao, J. / Ye, M. / Araki, M. / Matsumoto, K. / Yamamoto, N. / Sugimoto, T. / Yoshikawa, Y. / Kumasaka, T. / Yamamoto, M. / Tamura, A. / Kataoka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kkm.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kkm.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kkm_validation.pdf.gz | 762 KB | Display | wwPDB validaton report |
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Full document | 3kkm_full_validation.pdf.gz | 763.4 KB | Display | |
Data in XML | 3kkm_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3kkm_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/3kkm ftp://data.pdbj.org/pub/pdb/validation_reports/kk/3kkm | HTTPS FTP |
-Related structure data
Related structure data | 3kknC 3kkoC 3kkpC 3kkqC 5p21S 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 on special symmetry positions |
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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#1: Protein | Mass: 19387.707 Da / Num. of mol.: 1 / Fragment: G domain, UNP residues 1-166 / Mutation: T35S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): AG-1 / References: UniProt: P01112 | ||
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#2: Chemical | ChemComp-GNP / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #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: 2.51 Å3/Da / Density % sol: 51.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris-HCl, Ammonium Sulfate, DMSO, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 10, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27.59 Å / Num. all: 21625 / Num. obs: 21625 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 43.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2139 / Rsym value: 0.295 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5P21 Resolution: 1.7→23.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.818 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / 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: 19.911 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→23.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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