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- PDB-2kio: NMR structure of the oxidized yeast TOR1 FATC domain bound to DPC... -

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Basic information

Entry
Database: PDB / ID: 2kio
TitleNMR structure of the oxidized yeast TOR1 FATC domain bound to DPC micelles at 318K
ComponentsSerine/threonine-protein kinase TOR1
KeywordsTRANSFERASE / protein / dpc micelle / membrane-mimetic / ATP-binding / Cell cycle / Cell membrane / Kinase / Membrane / Nucleotide-binding / Serine/threonine-protein kinase / Vacuole
Function / homology
Function and homology information


regulation of snRNA pseudouridine synthesis / regulation of sphingolipid biosynthetic process / mitochondria-nucleus signaling pathway / fungal-type cell wall organization / TORC2 complex / TORC1 complex / TORC1 signaling / fungal-type vacuole membrane / cellular response to nitrogen starvation / negative regulation of macroautophagy ...regulation of snRNA pseudouridine synthesis / regulation of sphingolipid biosynthetic process / mitochondria-nucleus signaling pathway / fungal-type cell wall organization / TORC2 complex / TORC1 complex / TORC1 signaling / fungal-type vacuole membrane / cellular response to nitrogen starvation / negative regulation of macroautophagy / nucleolar large rRNA transcription by RNA polymerase I / TOR signaling / response to endoplasmic reticulum stress / negative regulation of autophagy / response to nutrient / meiotic cell cycle / regulation of cell growth / translational initiation / ribosome biogenesis / cellular response to heat / cellular response to oxidative stress / regulation of cell cycle / non-specific serine/threonine protein kinase / endosome membrane / protein kinase activity / protein phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / protein-containing complex binding / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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 / : / FATC 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 / : / 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 / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase TOR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsDames, S.A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Basis for the Association of the Redox-sensitive Target of Rapamycin FATC Domain with Membrane-mimetic Micelles.
Authors: Dames, S.A.
History
DepositionMay 7, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 15, 2017Group: Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_assembly ...pdbx_database_related / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_related.db_name
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase TOR1


Theoretical massNumber of molelcules
Total (without water)3,9631
Polymers3,9631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3410 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Serine/threonine-protein kinase TOR1 / Phosphatidylinositol kinase homolog TOR1 / Target of rapamycin kinase 1 / Dominant rapamycin ...Phosphatidylinositol kinase homolog TOR1 / Target of rapamycin kinase 1 / Dominant rapamycin resistance protein 1


Mass: 3963.473 Da / Num. of mol.: 1 / Fragment: yeast TOR1 FATC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DRR1, J1803, TOR1, YJR066W / Plasmid: pGEV2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Rosetta (DE3)
References: UniProt: P35169, non-specific serine/threonine protein kinase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-15N HSQC
1412D 1H-13C HSQC
1513D HNCA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1923D 1H-13C NOESY
11013D HNHB
111113C'-{13Cg} SED 1H-15N HSQC
112115N-{13Cg} SED 1H-15N HSQC
1131{15N} SED 1H-13C HSQC
1141{13C'} SED 1H-13C HSQC
115115N T1
116115N T2
1171{1H}-15N-NOE

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Sample preparation

Details
Solution-IDContents
10.40-0.46 mM [U-13C; U-15N] y1fatc-1
20.40 mM [U-13C; U-15N] y1fatc-2
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMy1fatc-1[U-13C; U-15N]0.40-0.461
0.40 mMy1fatc-2[U-13C; U-15N]2
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
NMRView5.2.2_01Johnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ProcheckNMRLaskowski and MacArthurstructure analysis
MOLMOLKoradi, Billeter and Wuthrichstructure visualization
XwinNMR3.5Bruker Biospinprocessing
TENSOR22P. Dosset, D. Marion, M. Blackledgeanalysis of 15n relaxation data
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 932 / Disulfide bond constraints total count: 1 / Protein chi angle constraints total count: 15 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 21
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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