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Yorodumi- PDB-4fap: ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH H... -
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-Basic information
Entry | Database: PDB / ID: 4fap | ||||||
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Title | ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN FKBP12 AND FRB DOMAIN OF FRAP | ||||||
Components |
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Keywords | CELL 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 / 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 / regulation of membrane permeability / heart valve morphogenesis / 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 / cellular response to L-leucine / signaling receptor inhibitor activity / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / type I transforming growth factor beta receptor binding / energy reserve metabolic process / Energy dependent regulation of mTOR by LKB1-AMPK / nucleus localization / negative regulation of activin receptor signaling pathway / ruffle organization / heart trabecula formation / negative regulation of cell size / cellular response to osmotic stress / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / anoikis / cardiac muscle cell development / negative regulation of protein localization to nucleus / positive regulation of transcription by RNA polymerase III / 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 / negative regulation of phosphoprotein phosphatase activity / positive regulation of oligodendrocyte differentiation / 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 / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / cellular response to nutrient levels / CD28 dependent PI3K/Akt signaling / positive regulation of translational initiation / positive regulation of phosphoprotein phosphatase activity / neuronal action potential / Calcineurin activates NFAT / HSF1-dependent transactivation / regulation of macroautophagy / positive regulation of epithelial to mesenchymal transition / endomembrane system / regulation of immune response / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / protein peptidyl-prolyl isomerization / supramolecular fiber organization / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of lipid biosynthetic process / regulation of cellular response to heat / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / cardiac muscle contraction / positive regulation of stress fiber assembly / cytoskeleton organization / sarcoplasmic reticulum membrane / cellular response to amino acid starvation / T cell costimulation / cellular response to starvation / positive regulation of glycolytic process / T cell activation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liang, 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fap.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fap.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/4fap ftp://data.pdbj.org/pub/pdb/validation_reports/fa/4fap | HTTPS FTP |
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-Related structure data
Related structure data | 1nsgC 2fapSC 3fapC 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) / 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 |
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#2: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 8 Details: 20% PEG8000, 10% MPD, 0.1 M TRIS-HCL PH 8.5, pH 8.0 |
Crystal grow | *PLUS Method: otherDetails: This particular structure is not described in this paper. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Feb 1, 1997 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.96 Å2 / ksol: 0.271 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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