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Yorodumi- PDB-6yf1: FKBP12 in complex with the BMP potentiator compound 8 at 1.12A re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yf1 | ||||||
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Title | FKBP12 in complex with the BMP potentiator compound 8 at 1.12A resolution | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP1A | ||||||
Keywords | ISOMERASE / IMMUNOSUPPRESSION / IMMUNOSUPPRESSANT / BMP ENHANCER PROGRAM | ||||||
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 / heart trabecula formation / terminal cisterna ...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 / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / 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 / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transmembrane transporter binding / amyloid fibril formation / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 Å | ||||||
Authors | Kallen, J. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2021 Title: Phenotypic screen identifies calcineurin-sparing FK506 analogs as BMP potentiators for treatment of acute kidney injury. Authors: Larraufie, M.H. / Gao, X. / Xia, X. / Devine, P.J. / Kallen, J. / Liu, D. / Michaud, G. / Harsch, A. / Savage, N. / Ding, J. / Tan, K. / Mihalic, M. / Roggo, S. / Canham, S.M. / Bushell, S.M. ...Authors: Larraufie, M.H. / Gao, X. / Xia, X. / Devine, P.J. / Kallen, J. / Liu, D. / Michaud, G. / Harsch, A. / Savage, N. / Ding, J. / Tan, K. / Mihalic, M. / Roggo, S. / Canham, S.M. / Bushell, S.M. / Krastel, P. / Gao, J. / Izaac, A. / Altinoglu, E. / Lustenberger, P. / Salcius, M. / Harbinski, F. / Williams, E.T. / Zeng, L. / Loureiro, J. / Cong, F. / Fryer, C.J. / Klickstein, L. / Tallarico, J.A. / Jain, R.K. / Rothman, D.M. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yf1.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yf1.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 6yf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/6yf1 ftp://data.pdbj.org/pub/pdb/validation_reports/yf/6yf1 | HTTPS FTP |
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-Related structure data
Related structure data | 6yf0C 6yf2C 6yf3C 4dh0S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11990.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P62942, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-OP8 / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.2 M AmSO4, 0.2 M CdCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2015 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→17.18 Å / Num. obs: 37030 / % possible obs: 94.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.046 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.12→1.15 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2265 / Rrim(I) all: 0.477 / % possible all: 79.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DH0 Resolution: 1.12→17.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.914 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.034 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 51.19 Å2 / Biso mean: 15.209 Å2 / Biso min: 6.86 Å2
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Refinement step | Cycle: final / Resolution: 1.12→17.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.124→1.153 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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