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- PDB-1w1n: The solution structure of the FATC Domain of the Protein Kinase T... -

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Basic information

Entry
Database: PDB / ID: 1w1n
TitleThe solution structure of the FATC Domain of the Protein Kinase TOR1 from yeast
ComponentsPHOSPHATIDYLINOSITOL 3-KINASE TOR1
KeywordsTRANSFERASE / TOR / TARGET OF RAPAMYCIN / SER/THR KINASE / REDOX-REGULATION / DISULFIDE BOND
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 / RESTRAINED TORSION ANGLE MOLECULAR DYNAMICS
AuthorsDames, S.A. / Mulet, J.M. / Rathgeb-Szabo, K. / Hall, M.N. / Grzesiek, S.
CitationJournal: J. Biol. Chem. / Year: 2005
Title: The solution structure of the FATC domain of the protein kinase target of rapamycin suggests a role for redox-dependent structural and cellular stability.
Authors: Dames, S.A. / Mulet, J.M. / Rathgeb-Szabo, K. / Hall, M.N. / Grzesiek, S.
History
DepositionJun 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_sample_details
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-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_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST ENERGY AND LEAST RESTRAINED VIOLATION
RepresentativeModel #2

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Components

#1: Protein/peptide PHOSPHATIDYLINOSITOL 3-KINASE TOR1 / PI3-KINASE RELATED / PTDINS-3-KINASE RELATED / PI3K RELATED


Mass: 3963.473 Da / Num. of mol.: 1 / Fragment: FATC, RESIDUES 2438-2470
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BOND BETWEEN RESIDUES C2460 (23) AND C2467 (30)
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P35169, phosphatidylinositol 3-kinase
Compound detailsPHOSPHATIDYLINOSITOL 3-KINASE HOMOLOG REQUIRED FOR G1 PROGRESSION. TARGET OF THE ANTIBIOTIC RAPAMYCIN.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC
1213D-CBCANH
1313D CBCA(CO)NH
1413D-HBHACBCACONH
1513D-C(CO)NH-TOCSY
1613D HNCO
1713D HNHA
1813D-15N-NOESY
1913D-15N- ROESY
110113CO-13CG -HSQC
111115N- 13CG-HSQC
112115N-T1
113115N-T2
11411H- 15N-NOE
215113-HSQC
21613D-13C- NOESY
21713D (H)CCH-TOCSY
21813D- HACAHB-COSY
319115N-IPAP- HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTINUCLEAR NMR EXPERIMENTS ON 15- OR 15N-13C-LABELED YEAST TOR1 FATC.

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Sample preparation

Details
TypeSolution-IDLabelSolvent system
solution1sample_195% H2O/5% D2O
solution2sample_2100% D2O
solution3sample_295% H2O/ 5% D2O and PF1 phages
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mMsample_161.0 atm298.0 K
210 mMsample_261.0 atm298.0 K
310 mMsample_361.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHBRUNGER, SCHWIETERSrefinement
Xplor-NIHstructure solution
NMRViewstructure solution
RefinementMethod: RESTRAINED TORSION ANGLE MOLECULAR DYNAMICS / Software ordinal: 1
Details: SHIFTS HAVE BEEN DEPOSITED AT BMRB UNDER ACCESSION NUMBER 6228
NMR ensembleConformer selection criteria: LOWEST ENERGY AND LEAST RESTRAINED VIOLATION
Conformers calculated total number: 200 / Conformers submitted total number: 20

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