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- PDB-5gpg: Co-crystal structure of the FK506 binding domain of human FKBP25,... -

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Basic information

Entry
Database: PDB / ID: 5gpg
TitleCo-crystal structure of the FK506 binding domain of human FKBP25, Rapamycin and the FRB domain of human mTOR
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP3
  • Serine/threonine-protein kinase mTOR
KeywordsISOMERASE/TRANSFERASE / complex / kinase / ISOMERASE-TRANSFERASE complex
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability ...RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / negative regulation of lysosome organization / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / TORC1 complex / voluntary musculoskeletal movement / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of osteoclast differentiation / regulation of lysosome organization / MTOR signalling / cellular response to nutrient / cellular response to L-leucine / Amino acids regulate mTORC1 / energy reserve metabolic process / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / ruffle organization / serine/threonine protein kinase complex / cellular response to methionine / negative regulation of cell size / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / inositol hexakisphosphate binding / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / Macroautophagy / positive regulation of myotube differentiation / FK506 binding / regulation of cell size / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / germ cell development / TOR signaling / behavioral response to pain / mTORC1-mediated signalling / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / regulation of macroautophagy / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of epithelial to mesenchymal transition / vascular endothelial cell response to laminar fluid shear stress / positive regulation of lipid biosynthetic process / heart morphogenesis / cellular response to nutrient levels / neuronal action potential / regulation of cellular response to heat / positive regulation of lamellipodium assembly / cardiac muscle contraction / phagocytic vesicle / T cell costimulation / positive regulation of stress fiber assembly / cytoskeleton organization / endomembrane system / negative regulation of insulin receptor signaling pathway / negative regulation of autophagy / cellular response to amino acid starvation / positive regulation of translation / regulation of signal transduction by p53 class mediator / positive regulation of glycolytic process / cellular response to starvation / Regulation of PTEN gene transcription / VEGFR2 mediated vascular permeability / post-embryonic development / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / peptidylprolyl isomerase / cellular response to amino acid stimulus / non-specific protein-tyrosine kinase / peptidyl-prolyl cis-trans isomerase activity / macroautophagy / response to nutrient levels / phosphoprotein binding / regulation of cell growth / regulation of circadian rhythm / PML body / protein destabilization / response to virus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase FKBP3 / FKBP3, basic tilted helix bundle domain / Basic tilted helix bundle 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 ...Peptidyl-prolyl cis-trans isomerase FKBP3 / FKBP3, basic tilted helix bundle domain / Basic tilted helix bundle 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 / Chitinase A; domain 3 - #40 / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Chitinase A; domain 3 / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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
RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Serine/threonine-protein kinase mTOR / Peptidyl-prolyl cis-trans isomerase FKBP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsLee, H.B. / Lee, S.Y. / Rhee, H.W. / Lee, C.W.
CitationJournal: Acs Cent.Sci. / Year: 2016
Title: Proximity-Directed Labeling Reveals a New Rapamycin-Induced Heterodimer of FKBP25 and FRB in Live Cells
Authors: Lee, S.Y. / Lee, H. / Lee, H.K. / Lee, S.W. / Ha, S.C. / Kwon, T. / Seo, J.K. / Lee, C. / Rhee, H.W.
History
DepositionAug 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP3
B: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3143
Polymers24,4002
Non-polymers9141
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-5 kcal/mol
Surface area10960 Å2
Unit cell
Length a, b, c (Å)46.038, 58.352, 86.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP3 / PPIase FKBP3 / 25 kDa FK506-binding protein / FKBP-25 / FK506-binding protein 3 / FKBP-3 / ...PPIase FKBP3 / 25 kDa FK506-binding protein / FKBP-25 / FK506-binding protein 3 / FKBP-3 / Immunophilin FKBP25 / Rapamycin-selective 25 kDa immunophilin / Rotamase


Mass: 13047.042 Da / Num. of mol.: 1 / Fragment: UNP residues 109-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP3, FKBP25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q00688, 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: 11352.787 Da / Num. of mol.: 1 / Fragment: UNP residues 2021-2112
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


Mass: 914.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H79NO13 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% polyethyleneglycol 8000, 100mM sodium cacodylate, 200mM sodium acetate, 10mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.669→50 Å / Num. obs: 27591 / % possible obs: 99.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 27.1
Reflection shellResolution: 1.67→1.7 Å / Rmerge(I) obs: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
Cootmodel building
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBK, 1FAP

1pbk

1fap


Resolution: 1.67→27.73 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7
RfactorNum. reflection% reflection
Rfree0.212 1380 5 %
Rwork0.174 --
obs0.176 27591 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.67→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 65 288 2009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061766
X-RAY DIFFRACTIONf_angle_d1.0472379
X-RAY DIFFRACTIONf_dihedral_angle_d15.423681
X-RAY DIFFRACTIONf_chiral_restr0.044250
X-RAY DIFFRACTIONf_plane_restr0.004299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6685-1.72820.27141330.21792533X-RAY DIFFRACTION97
1.7282-1.79730.26831330.21522537X-RAY DIFFRACTION99
1.7973-1.87910.25741370.20162585X-RAY DIFFRACTION99
1.8791-1.97820.23421360.18682593X-RAY DIFFRACTION99
1.9782-2.10210.18931380.17212610X-RAY DIFFRACTION99
2.1021-2.26430.20851370.1682606X-RAY DIFFRACTION100
2.2643-2.4920.21271390.17462626X-RAY DIFFRACTION100
2.492-2.85230.22091390.18152660X-RAY DIFFRACTION100
2.8523-3.59240.18151410.16512678X-RAY DIFFRACTION100
3.5924-27.7380.20771470.15572783X-RAY DIFFRACTION99

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