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Yorodumi- PDB-6m4u: Crystal structure of FKBP-FRB T2098L mutant in complex with rapamycin -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m4u | |||||||||
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Title | Crystal structure of FKBP-FRB T2098L mutant in complex with rapamycin | |||||||||
Components |
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Keywords | ISOMERASE / Rapamycin / complex / kinase | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Kikuchi, M. / Wu, D. / Inoue, T. / Umehara, T. | |||||||||
Citation | Journal: Nat.Methods / Year: 2020 Title: Rational design and implementation of a chemically inducible heterotrimerization system. Authors: Wu, H.D. / Kikuchi, M. / Dagliyan, O. / Aragaki, A.K. / Nakamura, H. / Dokholyan, N.V. / Umehara, T. / Inoue, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m4u.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m4u.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 6m4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m4u_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6m4u_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6m4u_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 6m4u_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m4u ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m4u | HTTPS FTP |
-Related structure data
Related structure data | 6m4vC 6m4wC 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules AEBF
#1: Protein | Mass: 12111.834 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase #2: Protein | Mass: 11447.091 Da / Num. of mol.: 2 / Mutation: T2098L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR / Production host: Escherichia coli (E. coli) References: UniProt: P42345, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 332 molecules
#3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM cacodylic acid buffer (pH 6.5), 350 mM zinc acetate and 8% (w/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.45 Å / Num. obs: 24948 / % possible obs: 96.6 % / Redundancy: 6.9 % / CC1/2: 0.995 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.2→2.27 Å / Num. unique obs: 2223 / CC1/2: 0.849 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FAP Resolution: 2.2→47.4 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.305 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.232 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.727 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→47.4 Å
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