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- PDB-4fap: ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH H... -

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Basic information

Entry
Database: PDB / ID: 4fap
TitleATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN FKBP12 AND FRB DOMAIN OF FRAP
Components
  • FK506-BINDING PROTEIN
  • FKBP12-RAPAMYCIN ASSOCIATED PROTEIN
KeywordsCELL CYCLE / FKBP12 / FRAP / RAPAMYCIN / COMPLEX / GENE THERAPY
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
C15-(R)-METHYLTHIENYL RAPAMYCIN / Serine/threonine-protein kinase mTOR / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiang, J. / Clardy, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution.
Authors: Liang, J. / Choi, J. / Clardy, J.
History
DepositionMay 6, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FK506-BINDING PROTEIN
B: FKBP12-RAPAMYCIN ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1493
Polymers23,1682
Non-polymers9801
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.400, 52.100, 102.560
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 FK506-BINDING PROTEIN / FKBP12


Mass: 11836.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 (DE3) (NOVAGEN)
Gene: HUMAN HIPPOCAMPAL CDNA LIBRARY SOURCE 8 (CLONTECH, PALO ALTO, CA)
Plasmid: PGEX-3X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) (NOVAGEN) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Protein FKBP12-RAPAMYCIN ASSOCIATED PROTEIN / FRAP


Mass: 11331.937 Da / Num. of mol.: 1 / Fragment: FRB / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42345
#3: Chemical ChemComp-ARD / C15-(R)-METHYLTHIENYL RAPAMYCIN / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


Mass: 980.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H81NO12S / Comment: antibiotic*YM

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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: 2.62 Å3/Da / Density % sol: 50 %
Crystal growpH: 8
Details: 20% PEG8000, 10% MPD, 0.1 M TRIS-HCL PH 8.5, pH 8.0
Crystal grow
*PLUS
Method: other
Details: This particular structure is not described in this paper.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Feb 1, 1997
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 5598 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 8.6 / Net I/σ(I): 10.4

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Processing

Software
NameClassification
CNSrefinement
UCSD-systemdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FAP

2fap


Resolution: 2.8→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high rms absF: 72314.66 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 480 9.9 %RANDOM
Rwork0.184 ---
obs-4851 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.96 Å2 / ksol: 0.271 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-19.13 Å20 Å20 Å2
2---5.9 Å20 Å2
3----13.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 69 0 1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it8.151.5
X-RAY DIFFRACTIONc_mcangle_it11.662
X-RAY DIFFRACTIONc_scbond_it11.412
X-RAY DIFFRACTIONc_scangle_it16.452.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 324 9.8 %
Rwork0.266 0 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION21703.PAR1703.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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