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- PDB-2gaq: NMR SOLUTION STRUCTURE OF THE FRB DOMAIN OF mTOR -

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Basic information

Entry
Database: PDB / ID: 2gaq
TitleNMR SOLUTION STRUCTURE OF THE FRB DOMAIN OF mTOR
ComponentsFKBP12-rapamycin complex-associated protein
KeywordsTRANSFERASE / four helical up and down bundle
Function / homology
Function and homology information


cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 complex ...cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / regulation of lysosome organization / TORC1 complex / negative regulation of lysosome organization / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / MTOR signalling / cellular response to L-leucine / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / regulation of autophagosome assembly / Amino acids regulate mTORC1 / Dengue virus modulates apoptosis / cellular response to methionine / TORC2 signaling / cellular response to osmotic stress / TORC1 signaling / anoikis / inositol hexakisphosphate binding / negative regulation of protein localization to nucleus / positive regulation of ubiquitin-dependent protein catabolic process / regulation of cell size / negative regulation of macroautophagy / Macroautophagy / Constitutive Signaling by AKT1 E17K in Cancer / behavioral response to pain / positive regulation of transcription by RNA polymerase III / positive regulation of protein kinase activity / response to amino acid / neuronal action potential / TOR signaling / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / positive regulation of translational initiation / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / T cell costimulation / vascular endothelial cell response to laminar fluid shear stress / regulation of cellular response to heat / cellular response to nutrient levels / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / cytoskeleton organization / negative regulation of insulin receptor signaling pathway / phagocytic vesicle / endomembrane system / positive regulation of glycolytic process / negative regulation of autophagy / cellular response to amino acid stimulus / regulation of signal transduction by p53 class mediator / cellular response to amino acid starvation / cellular response to starvation / Regulation of PTEN gene transcription / phosphatidylinositol 3-kinase/protein kinase B signal transduction / VEGFR2 mediated vascular permeability / regulation of actin cytoskeleton organization / positive regulation of translation / TP53 Regulates Metabolic Genes / non-specific protein-tyrosine kinase / regulation of cell growth / non-membrane spanning protein tyrosine kinase activity / phosphoprotein binding / response to nutrient levels / PML body / regulation of circadian rhythm / cellular response to insulin stimulus / Regulation of TP53 Degradation / PIP3 activates AKT signaling / nuclear envelope / positive regulation of cell growth / response to heat / ribosome binding / protein tyrosine kinase activity / cellular response to hypoxia / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transmembrane transporter binding / protein kinase activity / protein phosphorylation / mitochondrial outer membrane / non-specific serine/threonine protein kinase / lysosome / protein stabilization / inflammatory response / Golgi membrane / protein serine kinase activity
Similarity search - Function
FKBP12-rapamycin binding domain / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / : ...FKBP12-rapamycin binding domain / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / : / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics energy minimization
AuthorsLeone, M. / Pellecchia, M.
CitationJournal: Biochemistry / Year: 2006
Title: The FRB Domain of mTOR: NMR Solution Structure and Inhibitor Design.
Authors: Leone, M. / Crowell, K.J. / Chen, J. / Jung, D. / Chiang, G.G. / Sareth, S. / Abraham, R.T. / Pellecchia, M.
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FKBP12-rapamycin complex-associated protein


Theoretical massNumber of molelcules
Total (without water)12,1021
Polymers12,1021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein FKBP12-rapamycin complex-associated protein / FK506-binding protein 12- rapamycin complex-associated protein 1 / Rapamycin target protein / RAPT1 ...FK506-binding protein 12- rapamycin complex-associated protein 1 / Rapamycin target protein / RAPT1 / Mammalian target of rapamycin / MTOR


Mass: 12101.867 Da / Num. of mol.: 1 / Fragment: FRB DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRAP1, FRAP, FRAP2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42345

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
1222D TOCSY
1313D 15N-separated NOESY
1413D-(1H,1H,15N) -TOCSY
153HNCA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM FRB U-15NPBS 10% D2O 90% H2O
20.5 mM FRB U-15NPBS 100%D2O
30.6 mM FRB U-15N, U-13CPBS 10% D2O 90% H2O
Sample conditionsIonic strength: 20 mM PBS 1 mM DTT / pH: 7.4 / Pressure: ambient / Temperature: 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntertstructure solution
GROMOS96Van Gunsterenrefinement
RefinementMethod: torsion angle dynamics energy minimization / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 19

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