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- PDB-2rse: NMR structure of FKBP12-mTOR FRB domain-rapamycin complex structu... -

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Basic information

Entry
Database: PDB / ID: 2rse
TitleNMR structure of FKBP12-mTOR FRB domain-rapamycin complex structure determined based on PCS
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Serine/threonine-protein kinase mTOR
KeywordsISOMERASE/TRANSFERASE / FKBP12 / rapamycin / FK506 / lanthanide / PCS / ISOMERASE-TRANSFERASE complex
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex ...RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex / regulation of membrane permeability / heart valve morphogenesis / macrolide binding / negative regulation of lysosome organization / activin receptor binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / TORC1 complex / cytoplasmic side of membrane / calcineurin-NFAT signaling cascade / nucleus localization / cellular response to methionine / voluntary musculoskeletal movement / regulation of osteoclast differentiation / TORC1 signaling / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / signaling receptor inhibitor activity / positive regulation of keratinocyte migration / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / type I transforming growth factor beta receptor binding / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / energy reserve metabolic process / negative regulation of activin receptor signaling pathway / heart trabecula formation / negative regulation of cell size / ruffle organization / terminal cisterna / ryanodine receptor complex / cellular response to osmotic stress / I-SMAD binding / negative regulation of protein localization to nucleus / regulation of amyloid precursor protein catabolic process / anoikis / cardiac muscle cell development / protein maturation by protein folding / positive regulation of transcription by RNA polymerase III / ventricular cardiac muscle tissue morphogenesis / negative regulation of calcineurin-NFAT signaling cascade / 'de novo' protein folding / regulation of myelination / negative regulation of macroautophagy / regulation of cell size / positive regulation of oligodendrocyte differentiation / FK506 binding / Macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / oligodendrocyte differentiation / behavioral response to pain / channel regulator activity / TGF-beta receptor signaling activates SMADs / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / : / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / HSF1-dependent transactivation / neuronal action potential / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / TOR signaling / response to amino acid / endomembrane system / cellular response to nutrient levels / positive regulation of translational initiation / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lamellipodium assembly / positive regulation of epithelial to mesenchymal transition / positive regulation of lipid biosynthetic process / heart morphogenesis / cardiac muscle contraction / supramolecular fiber organization / regulation of cellular response to heat / phagocytic vesicle / positive regulation of stress fiber assembly / cytoskeleton organization / sarcoplasmic reticulum membrane / T cell costimulation / T cell activation / cellular response to starvation
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 / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / Chitinase A; domain 3 - #40 / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Roll / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TERBIUM(III) ION / Serine/threonine-protein kinase mTOR / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKobashigawa, Y. / Ushio, M. / Saio, T. / Inagaki, F.
CitationJournal: J.Biomol.Nmr / Year: 2012
Title: Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein-protein complex structure determination.
Authors: Kobashigawa, Y. / Saio, T. / Ushio, M. / Sekiguchi, M. / Yokochi, M. / Ogura, K. / Inagaki, F.
History
DepositionJan 25, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4864
Polymers23,1682
Non-polymers3182
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / FK506-binding protein 1A / ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 11836.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Protein Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1


Mass: 11331.937 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2019-2112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: PCS-based rigid body docking structure
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.3 mM FKBP12-1, 0.3 mM [U-98% 15N] FRB-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMFKBP12-11
0.3 mMFRB-2[U-98% 15N]1
Sample conditionsIonic strength: 0.15 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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