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- PDB-3fap: ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH H... -
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Basic information
Entry | Database: PDB / ID: 3fap | ||||||
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Title | ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN FKBP12 AND FRB DOMAIN OF FRAP | ||||||
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![]() | CELL CYCLE / FKBP12 / FRAP / RAPAMYCIN / COMPLEX / GENE THERAPY | ||||||
Function / homology | ![]() positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / regulation of membrane permeability / TFIIIC-class transcription factor complex binding ...positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / regulation of membrane permeability / TFIIIC-class transcription factor complex binding / heart valve morphogenesis / negative regulation of lysosome organization / macrolide binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC2 complex / activin receptor binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / cytoplasmic side of membrane / regulation of autophagosome assembly / calcineurin-NFAT signaling cascade / nucleus localization / TORC1 signaling / voluntary musculoskeletal movement / regulation of osteoclast differentiation / positive regulation of keratinocyte migration / signaling receptor inhibitor activity / 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 / energy reserve metabolic process / type I transforming growth factor beta receptor binding / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of activin receptor signaling pathway / negative regulation of cell size / heart trabecula formation / ruffle organization / cellular response to osmotic stress / terminal cisterna / ryanodine receptor complex / I-SMAD binding / negative regulation of protein localization to nucleus / anoikis / regulation of amyloid precursor protein catabolic process / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / protein maturation by protein folding / negative regulation of calcineurin-NFAT signaling cascade / ventricular cardiac muscle tissue morphogenesis / 'de novo' protein folding / regulation of myelination / regulation of cell size / Macroautophagy / negative regulation of phosphoprotein phosphatase activity / positive regulation of oligodendrocyte differentiation / negative regulation of macroautophagy / FK506 binding / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / behavioral response to pain / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / germ cell development / CD28 dependent PI3K/Akt signaling / cellular response to nutrient levels / positive regulation of phosphoprotein phosphatase activity / Calcineurin activates NFAT / HSF1-dependent transactivation / regulation of immune response / TOR signaling / neuronal action potential / positive regulation of translational initiation / response to amino acid / regulation of macroautophagy / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / protein peptidyl-prolyl isomerization / 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 / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of stress fiber assembly / cytoskeleton organization / sarcoplasmic reticulum membrane / T cell costimulation / T cell activation / cellular response to amino acid starvation / phagocytic vesicle / positive regulation of glycolytic process / cellular response to starvation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liang, J. / Clardy, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.6 KB | Display | ![]() |
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PDB format | ![]() | 43.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 888.4 KB | Display | ![]() |
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Full document | ![]() | 907.2 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nsgC ![]() 2fapSC ![]() 4fapC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: HUMAN HIPPOCAMPAL CDNA LIBRARY SOURCE 8 (CLONTECH, PALO ALTO, CA) Plasmid: PGEX-3X / Production host: ![]() ![]() |
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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) ![]() |
#3: Chemical | ChemComp-ARD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 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 8.00 |
Crystal grow | *PLUS Method: otherDetails: This particular structure is not described in this paper. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Feb 1, 1999 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100 Å / Num. obs: 20139 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 4.7 / Net I/σ(I): 10.4 |
Reflection shell | Highest resolution: 1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.3 / Rsym value: 28.7 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FAP Resolution: 1.85→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1024989.71 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.54 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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