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Yorodumi- PDB-2clc: CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN ... -
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-Basic information
Entry | Database: PDB / ID: 2clc | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GTP (2) | ||||||
Components | GTPASE HRAS | ||||||
Keywords | NUCLEOTIDE-BINDING PROTEIN / GOLGI APPARATUS / PROTO-ONCOGENE / R-CAGED GTP / PRENYLATION / LIPOPROTEIN / GTP-BINDING / PALMITATE / METHYLATION | ||||||
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: 1.3 Å | ||||||
Authors | Klink, B.U. / Goody, R.S. / Scheidig, A.J. | ||||||
Citation | Journal: Biophys.J. / Year: 2006 Title: A Newly Designed Microspectrofluorometer for Kinetic Studies on Protein Crystals in Combination with X-Ray Diffraction Authors: Klink, B.U. / Goody, R.S. / Scheidig, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2clc.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2clc.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 2clc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2clc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2clc_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2clc_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 2clc_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/2clc ftp://data.pdbj.org/pub/pdb/validation_reports/cl/2clc | HTTPS FTP |
-Related structure data
Related structure data | 2ce2C 2cl0C 2cl6C 2cl7C 2cldC 2evwC 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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Number of models | 2 |
-Components
#1: Protein | Mass: 18799.096 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166 / Mutation: YES Source method: isolated from a genetically manipulated source Details: AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTAC RAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CK600K / References: UniProt: P01112 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-XY2 / | #4: Chemical | ChemComp-GTP / | #5: Water | ChemComp-HOH / | Compound details | RAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE ACTIVITY ENGINEERED RESIDUE IN CHAIN X, TYR ...RAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE ACTIVITY ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 100 MM HEPES PH 7.2, 200 MM MAGNESIUM ACETATE, 16% PEG ...Details: PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 100 MM HEPES PH 7.2, 200 MM MAGNESIUM ACETATE, 16% PEG 8000 FRESHLY PREPARED) MIXTURE OF EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 7, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→69.34 Å / Num. obs: 41195 / % possible obs: 100 % / Redundancy: 6.27 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.05 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.14 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5P21 Resolution: 1.3→69.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.301 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32. THE STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR THE WHOLE PROTEIN CHAIN. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32. THE STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR THE WHOLE PROTEIN CHAIN. THE CLOSE CONTACTS WITH WATER MOLECULES ARE CAUSED BY THE TREATMENT OF THE WHOLE PROTEIN CHAIN WITH TWO ALTERNATIVE CONFORMATIONS, BUT ONLY ONE POSITION PER WATER MOLECULE.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→69.34 Å
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