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Yorodumi- PDB-6m4w: Crystal structure of MBP fused split FKBP-FRB T2098L mutant in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m4w | ||||||
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Title | Crystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin | ||||||
Components |
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Keywords | ISOMERASE / Rapamycin / complex / kinase | ||||||
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 / detection of maltose stimulus / positive regulation of actin filament polymerization / maltose binding / maltose transport complex / maltose transport / positive regulation of myotube differentiation / behavioral response to pain / maltodextrin transmembrane transport / 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 / carbohydrate transmembrane transporter activity / Calcineurin activates NFAT / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / HSF1-dependent transactivation / carbohydrate transport / 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 Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 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 | 6m4w.cif.gz | 346.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m4w.ent.gz | 280.3 KB | Display | PDB format |
PDBx/mmJSON format | 6m4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m4w ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m4w | HTTPS FTP |
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-Related structure data
Related structure data | 6m4uC 6m4vC 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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3 |
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Unit cell |
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-Components
-Protein , 3 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 44074.879 Da / Num. of mol.: 3 / Mutation: D-288A, K-287A, E-198A, N-197A, K-131A Source method: isolated from a genetically manipulated source Details: This entity is chimeric. Organism is Homo sapiens and Eschrichia coli. Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human) Strain: K-12 / Gene: malE, b4034, JW3994, FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) References: UniProt: P0AEX9, UniProt: P62942, peptidylprolyl isomerase #2: Protein | Mass: 8486.715 Da / Num. of mol.: 3 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 #3: Protein | Mass: 11447.091 Da / Num. of mol.: 3 / 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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-Sugars , 1 types, 3 molecules
#4: Polysaccharide |
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-Non-polymers , 3 types, 195 molecules
#5: Chemical | #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: 2.95 Å3/Da / Density % sol: 58.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris-HCl buffer (pH 7.0), 200 mM calcium acetate and 20% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Dec 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.11→48.6 Å / Num. obs: 42250 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.992 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3.11→3.23 Å / Num. unique obs: 4337 / CC1/2: 0.522 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FAP Resolution: 3.11→48.65 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.88 / SU B: 27.493 / SU ML: 0.45 / Cross valid method: THROUGHOUT / ESU R Free: 0.517 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 70.304 Å2
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Refinement step | Cycle: 1 / Resolution: 3.11→48.65 Å
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