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Yorodumi- PDB-2fap: THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-(C16)-... -
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-Basic information
Entry | Database: PDB / ID: 2fap | ||||||
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Title | THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-(C16)-ETHOXY RAPAMYCIN COMPLEX INTERACTING WITH HUMA | ||||||
Components |
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Keywords | COMPLEX (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 / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / 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 / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / 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 / heart valve morphogenesis / regulation of membrane permeability / negative regulation of lysosome organization / macrolide binding / 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 / activin receptor binding / cytoplasmic side of membrane / regulation of autophagosome assembly / TORC1 signaling / voluntary musculoskeletal movement / regulation of osteoclast differentiation / positive regulation of keratinocyte migration / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / type I transforming growth factor beta receptor binding / cellular response to nutrient / energy reserve metabolic process / Energy dependent regulation of mTOR by LKB1-AMPK / nucleus localization / negative regulation of activin receptor signaling pathway / regulation of amyloid precursor protein catabolic process / ruffle organization / heart trabecula formation / negative regulation of cell size / cellular response to osmotic stress / terminal cisterna / ryanodine receptor complex / I-SMAD binding / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of protein localization to nucleus / protein maturation by protein folding / regulation of myelination / negative regulation of calcineurin-NFAT signaling cascade / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / Macroautophagy / regulation of cell size / negative regulation of macroautophagy / lysosome organization / positive regulation of oligodendrocyte differentiation / negative regulation of phosphoprotein phosphatase activity / FK506 binding / positive regulation of actin filament polymerization / positive regulation of myotube differentiation / behavioral response to pain / TOR signaling / oligodendrocyte differentiation / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / germ cell development / Constitutive Signaling by AKT1 E17K in Cancer / cellular response to nutrient levels / CD28 dependent PI3K/Akt signaling / positive regulation of phosphoprotein phosphatase activity / positive regulation of translational initiation / neuronal action potential / Calcineurin activates NFAT / HSF1-dependent transactivation / positive regulation of epithelial to mesenchymal transition / regulation of macroautophagy / endomembrane system / regulation of immune response / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / positive regulation of lipid biosynthetic process / protein peptidyl-prolyl isomerization / supramolecular fiber organization / phagocytic vesicle / positive regulation of lamellipodium assembly / heart morphogenesis / regulation of cellular response to heat / cytoskeleton organization / regulation of ryanodine-sensitive calcium-release channel activity / cardiac muscle contraction / positive regulation of stress fiber assembly / sarcoplasmic reticulum membrane / cellular response to amino acid starvation / T cell costimulation / cellular response to starvation / T cell activation / positive regulation of glycolytic process Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Liang, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fap.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fap.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/2fap ftp://data.pdbj.org/pub/pdb/validation_reports/fa/2fap | HTTPS FTP |
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-Related structure data
Related structure data | 1nsgC 3fapC 4fapC 1fapS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: 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 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 29, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 12865 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FAP Resolution: 2.2→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: RFREE / σ(F): 0
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Displacement parameters | Biso mean: 15.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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