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- PDB-2fap: THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-(C16)-... -

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Basic information

Entry
Database: PDB / ID: 2fap
TitleTHE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-(C16)-ETHOXY RAPAMYCIN COMPLEX INTERACTING WITH HUMA
Components
  • FK506-BINDING PROTEIN
  • FRAP
KeywordsCOMPLEX (ISOMERASE/KINASE) / FKBP12 / FRAP / RAPAMYCIN / COMPLEX (ISOMERASE-KINASE) / COMPLEX (ISOMERASE-KINASE) 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 / macrolide binding / negative regulation of lysosome organization / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / TORC1 complex / activin receptor binding / 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 skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of osteoclast differentiation / transforming growth factor beta receptor binding / cytoplasmic side of membrane / regulation of lysosome organization / MTOR signalling / TGFBR1 LBD Mutants in Cancer / cellular response to L-leucine / energy reserve metabolic process / type I transforming growth factor beta receptor binding / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / Amino acids regulate mTORC1 / TORC1 signaling / negative regulation of activin receptor signaling pathway / serine/threonine protein kinase complex / ruffle organization / cellular response to methionine / heart trabecula formation / negative regulation of cell size / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / regulation of amyloid precursor protein catabolic process / inositol hexakisphosphate binding / signaling receptor inhibitor activity / cardiac muscle cell development / terminal cisterna / ryanodine receptor complex / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / 'de novo' protein folding / negative regulation of macroautophagy / ventricular cardiac muscle tissue morphogenesis / 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 / behavioral response to pain / TOR signaling / TGF-beta receptor signaling activates SMADs / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / mTORC1-mediated signalling / positive regulation of translational initiation / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / regulation of macroautophagy / regulation of immune response / 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 / T cell costimulation / positive regulation of stress fiber assembly / phagocytic vesicle / supramolecular fiber organization / endomembrane system / cytoskeleton organization / negative regulation of insulin receptor signaling pathway / sarcoplasmic reticulum membrane / negative regulation of autophagy
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 / Serine/threonine-protein kinase ATR-like, HEAT repeats ...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
C49-METHYL 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: 2.2 Å
AuthorsLiang, J. / Choi, J. / Clardy, J.
Citation
Journal: 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.
#1: Journal: Science / Year: 1996
Title: Structure of the Fkbp12-Rapamycin Complex Interacting with the Binding Domain of Human Frap
Authors: Choi, J. / Chen, J. / Schreiber, S.L. / Clardy, J.
History
DepositionSep 22, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Derived calculations
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FK506-BINDING PROTEIN
B: FRAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,1682
Non-polymers9281
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.630, 52.140, 102.530
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) / Cell line: BL21
Gene: HUMAN HIPPOCAMPAL CDNA LIBRARY (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 FRAP / FKBP-RAPAMYCIN ASSOCIATED PROTEIN


Mass: 11331.937 Da / Num. of mol.: 1 / Fragment: FRB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HUMAN HIPPOCAMPAL CDNA LIBRARY / Plasmid: PGEX-3X / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42345
#3: Chemical ChemComp-RAD / C49-METHYL RAPAMYCIN


Mass: 928.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C52H81NO13 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.58 Å3/Da / Density % sol: 52 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
2150 mM1dropNaCl
315-20 %PEG80001reservoir
45-10 %MPD1reservoir
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 29, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 12865 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.27 / % possible all: 90.8
Reflection
*PLUS
Num. measured all: 30805
Reflection shell
*PLUS
% possible obs: 90.8 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
UCSDdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FAP

1fap


Resolution: 2.2→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: RFREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 -10 %RANDOM
Rwork0.196 ---
obs0.196 12865 97.4 %-
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 66 126 1820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg0.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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