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- PDB-1aue: FKBP-RAPAMYCIN BINDING DOMAIN (FRB) OF THE FKBP-RAPAMYCIN ASSOCIA... -

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Basic information

Entry
Database: PDB / ID: 1aue
TitleFKBP-RAPAMYCIN BINDING DOMAIN (FRB) OF THE FKBP-RAPAMYCIN ASSOCIATED PROTEIN
ComponentsFKBP-RAPAMYCIN ASSOCIATED PROTEIN
KeywordsTRANSFERASE / FKBP-RAPAMYCIN ASSOCIATED PROTEIN G1/S CELL CYCLE / KINASE
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 / 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 / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding ...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 / 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 / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / regulation of membrane permeability / heart valve morphogenesis / negative regulation of lysosome organization / nucleus localization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / regulation of osteoclast differentiation / voluntary musculoskeletal movement / TORC1 signaling / positive regulation of keratinocyte migration / cellular response to L-leucine / Amino acids regulate mTORC1 / MTOR signalling / cellular response to nutrient / cellular response to methionine / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of autophagosome assembly / energy reserve metabolic process / negative regulation of cell size / ruffle organization / cellular response to osmotic stress / anoikis / cardiac muscle cell development / negative regulation of protein localization to nucleus / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of actin filament polymerization / regulation of cell size / negative regulation of macroautophagy / positive regulation of oligodendrocyte differentiation / lysosome organization / Macroautophagy / positive regulation of myotube differentiation / behavioral response to pain / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / mTORC1-mediated signalling / germ cell development / CD28 dependent PI3K/Akt signaling / : / HSF1-dependent transactivation / neuronal action potential / response to amino acid / TOR signaling / 'de novo' pyrimidine nucleobase biosynthetic process / endomembrane system / regulation of macroautophagy / positive regulation of translational initiation / cellular response to nutrient levels / positive regulation of lamellipodium assembly / phagocytic vesicle / heart morphogenesis / positive regulation of lipid biosynthetic process / phosphorylation / positive regulation of epithelial to mesenchymal transition / cardiac muscle contraction / regulation of cellular response to heat / positive regulation of stress fiber assembly / cytoskeleton organization / T cell costimulation / cellular response to starvation / cellular response to amino acid starvation / post-embryonic development / positive regulation of glycolytic process / negative regulation of autophagy / response to nutrient / response to nutrient levels / VEGFR2 mediated vascular permeability / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / positive regulation of translation / regulation of cell growth / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / macroautophagy / phosphoprotein binding / protein destabilization / regulation of circadian rhythm / protein catabolic process / multicellular organism growth / PML body / cellular response to insulin stimulus / positive regulation of peptidyl-tyrosine phosphorylation / rhythmic process / Regulation of TP53 Degradation / PIP3 activates AKT signaling
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 / : / PIK-related kinase, FAT / FATC domain / FATC / FAT domain / FAT domain profile. / FATC domain profile. / FATC domain / PIK-related kinase / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsOdagaki, Y. / Clardy, J.
CitationJournal: J.Am.Chem.Soc. / Year: 1997
Title: Structural Basis for Peptidomimicry by the Effector Element of Rapamycin
Authors: Odagaki, Y. / Clardy, J.
History
DepositionAug 25, 1997Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 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: FKBP-RAPAMYCIN ASSOCIATED PROTEIN
B: FKBP-RAPAMYCIN ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,2042
Polymers24,2042
Non-polymers00
Water1,18966
1
A: FKBP-RAPAMYCIN ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,1021
Polymers12,1021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FKBP-RAPAMYCIN ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,1021
Polymers12,1021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.940, 59.210, 123.540
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 FKBP-RAPAMYCIN ASSOCIATED PROTEIN / FRAP / FRB


Mass: 12101.867 Da / Num. of mol.: 2 / Fragment: FKBP-RAPAMYCIN BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JURKAT TCELL CDNA LIBRARY / Plasmid: PGPX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42345
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROPS AT 4 C, pH 8.0, vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMTris-EDTA1drop
320 %(w/v)2-MPD1drop
410 %(w/v)PEG40001drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.01
DetectorType: PRINCETON 2K / Detector: CCD / Date: Feb 1, 1997
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.33→10 Å / Num. obs: 7307 / % possible obs: 73 % / Observed criterion σ(I): 2 / Redundancy: 1.73 % / Rsym value: 0.067 / Net I/σ(I): 6567.9
Reflection shellResolution: 2.33→2.42 Å / Redundancy: 1.12 % / Mean I/σ(I) obs: 1324 / % possible all: 28.9
Reflection
*PLUS
Rmerge(I) obs: 0.032

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAP

1fap


Resolution: 2.33→20 Å / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.339 -10 %RANDOM
Rwork0.232 ---
obs0.232 7218 72.1 %-
Displacement parametersBiso mean: 15.5 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 0 66 1644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.858
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.426 -
Rwork0.349 210
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.858

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