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Yorodumi- PDB-6m4v: Crystal structure of MBP fused split FKBP in complex with rapamycin -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m4v | ||||||
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Title | Crystal structure of MBP fused split FKBP in complex with rapamycin | ||||||
Components |
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Keywords | ISOMERASE / Rapamycin / complex / kinase | ||||||
Function / homology | Function and homology information macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / regulation of amyloid precursor protein catabolic process / heart trabecula formation ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / regulation of amyloid precursor protein catabolic process / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / carbohydrate transmembrane transporter activity / Calcineurin activates NFAT / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / ATP-binding cassette (ABC) transporter complex / T cell activation / cell chemotaxis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / outer membrane-bounded periplasmic space / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / periplasmic space / DNA damage response / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 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 | 6m4v.cif.gz | 381.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m4v.ent.gz | 310.9 KB | Display | PDB format |
PDBx/mmJSON format | 6m4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m4v ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m4v | HTTPS FTP |
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-Related structure data
Related structure data | 6m4uC 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
#1: Protein | Mass: 44074.879 Da / Num. of mol.: 2 / Mutation: K-131A, N-197A, E-198A, K-287A, D-288A 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.: 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 #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | 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: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Na-HEPES buffer (pH 7.5), 20% (w/v) PEG 8000 |
-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: Nov 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→48.14 Å / Num. obs: 23633 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.995 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.92→3.1 Å / Num. unique obs: 3775 / CC1/2: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FAP Resolution: 2.92→48.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.886 / SU B: 52.166 / SU ML: 0.483 / Cross valid method: THROUGHOUT / ESU R Free: 0.513 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: 52.568 Å2
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Refinement step | Cycle: 1 / Resolution: 2.92→48.14 Å
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