+Open data
-Basic information
Entry | Database: PDB / ID: 1xtr | ||||||
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Title | Structure of small GTPase human Rheb in complex with GppNHp | ||||||
Components | GTP-binding protein Rheb | ||||||
Keywords | SIGNALING PROTEIN / beta saddle / P-loop | ||||||
Function / homology | Function and homology information regulation of type B pancreatic cell development / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / Macroautophagy / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / protein kinase activator activity / oligodendrocyte differentiation ...regulation of type B pancreatic cell development / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / Macroautophagy / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / protein kinase activator activity / oligodendrocyte differentiation / mTORC1-mediated signalling / cellular response to nutrient levels / positive regulation of TOR signaling / regulation of macroautophagy / endomembrane system / positive regulation of TORC1 signaling / protein serine/threonine kinase activator activity / Regulation of PTEN gene transcription / TP53 Regulates Metabolic Genes / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spliceosomal complex / GDP binding / postsynaptic density / regulation of cell cycle / lysosomal membrane / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / protein kinase binding / magnesium ion binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Yu, Y. / Ding, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural Basis for the Unique Biological Function of Small GTPase RHEB Authors: Yu, Y. / Li, S. / Xu, X. / Li, Y. / Guan, K. / Arnold, E. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xtr.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xtr.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xtr_validation.pdf.gz | 758.2 KB | Display | wwPDB validaton report |
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Full document | 1xtr_full_validation.pdf.gz | 763.3 KB | Display | |
Data in XML | 1xtr_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1xtr_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/1xtr ftp://data.pdbj.org/pub/pdb/validation_reports/xt/1xtr | HTTPS FTP |
-Related structure data
Related structure data | 1xtqC 1xtsC 1guaS 1kaoS 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: 20148.965 Da / Num. of mol.: 1 / Fragment: GTPase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Rheb / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15382 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#4: Chemical | ChemComp-GOL / |
#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: 3.1 Å3/Da / Density % sol: 59.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: potassium dihydrogenphosphate, PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 17, 2004 / Details: osmic mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→12 Å / Num. all: 6973 / Num. obs: 6973 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.2 / Num. unique all: 714 / % possible all: 91.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1KAO, 1GUA Resolution: 2.65→12 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→12 Å
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Refine LS restraints |
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LS refinement shell |
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