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- PDB-1fap: THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMY... -

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Basic information

Entry
Database: PDB / ID: 1fap
TitleTHE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH HUMAN FRAP
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 / 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 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 / 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 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / macrolide binding / heart valve morphogenesis / activin receptor binding / negative regulation of lysosome organization / TFIIIC-class transcription factor complex binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / voluntary musculoskeletal movement / regulation of osteoclast differentiation / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / transforming growth factor beta receptor binding / regulation of lysosome organization / Amino acids regulate mTORC1 / TGFBR1 LBD Mutants in Cancer / cellular response to L-leucine / MTOR signalling / cellular response to nutrient / type I transforming growth factor beta receptor binding / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / energy reserve metabolic process / negative regulation of activin receptor signaling pathway / ruffle organization / serine/threonine protein kinase complex / negative regulation of cell size / heart trabecula formation / cellular response to methionine / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / inositol hexakisphosphate binding / cellular response to osmotic stress / signaling receptor inhibitor activity / regulation of amyloid precursor protein catabolic process / anoikis / terminal cisterna / ryanodine receptor complex / negative regulation of protein localization to nucleus / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / 'de novo' protein folding / positive regulation of actin filament polymerization / negative regulation of macroautophagy / ventricular cardiac muscle tissue morphogenesis / Macroautophagy / regulation of cell size / FK506 binding / positive regulation of myotube differentiation / Constitutive Signaling by AKT1 E17K in Cancer / oligodendrocyte differentiation / germ cell development / behavioral response to pain / TGF-beta receptor signaling activates SMADs / TOR signaling / mTORC1-mediated signalling / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / CD28 dependent PI3K/Akt signaling / response to amino acid / HSF1-dependent transactivation / regulation of macroautophagy / regulation of immune response / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to nutrient levels / vascular endothelial cell response to laminar fluid shear stress / neuronal action potential / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / regulation of cellular response to heat / positive regulation of lamellipodium assembly / supramolecular fiber organization / cardiac muscle contraction / phagocytic vesicle / positive regulation of stress fiber assembly / T cell costimulation / sarcoplasmic reticulum membrane / calcium channel regulator activity / cytoskeleton organization / endomembrane system / 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 / PIK-related kinase, FAT / FAT domain / Chitinase A; domain 3 - #40 / 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 domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / 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 FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsChoi, J. / Chen, J. / Schreiber, S.L. / Clardy, J.
CitationJournal: 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
DepositionMar 15, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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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)24,2403
Polymers23,3262
Non-polymers9141
Water41423
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 / Plasmid: PGEX-3X
Gene (production host): HUMAN HIPPOCAMPAL CDNA LIBRARY (CLONTECH, PALO ALTO, CA)
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: 11489.129 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 / Gene (production host): HUMAN HIPPOCAMPAL CDNA LIBRARY / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) (NOVAGEN) / References: UniProt: P42345
#3: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


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


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlFKBP121drop
260 mMTris-HCl1drop
510 mg/mlFRB1drop
6200 %(w/v)PEG80001reservoir
710 %methylpentanediol1reservoir
810 mMTris-HCl1reservoir
3rapamycin1drop
4methanol1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 29, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 6920 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.071
Reflection
*PLUS
Num. measured all: 43447

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
UCSDdata reduction
X-PLORphasing
RefinementResolution: 2.7→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.299 -10 %
Rwork0.193 --
obs0.193 6206 98 %
Displacement parametersBiso mean: 17.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 68 23 2108
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.48
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_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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