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Yorodumi- PDB-4n19: Structural basis of conformational transitions in the active site... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n19 | ||||||
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Title | Structural basis of conformational transitions in the active site and 80 s loop in the FK506 binding protein FKBP12 | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP1A | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information macrolide binding / activin receptor binding / cytoplasmic side of membrane / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / signaling receptor inhibitor activity / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / signaling receptor inhibitor activity / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / 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 / ventricular cardiac muscle tissue morphogenesis / 'de novo' protein folding / FK506 binding / channel regulator activity / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / negative regulation of transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / Z disc / regulation of protein localization / SARS-CoV-1 activates/modulates innate immune responses / protein folding / positive regulation of protein binding / positive regulation of canonical NF-kappaB signal transduction / protein refolding / Potential therapeutics for SARS / transmembrane transporter binding / amyloid fibril formation / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å | ||||||
Authors | Mustafi, S.M. / Brecher, M.B. / Zhang, J. / Li, H.M. / Lemaster, D.M. / Hernandez, G. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Structural basis of conformational transitions in the active site and 80's loop in the FK506-binding protein FKBP12. Authors: Mustafi, S.M. / Brecher, M. / Zhang, J. / Li, H. / Lemaster, D.M. / Hernandez, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n19.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n19.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 4n19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n19_validation.pdf.gz | 427.5 KB | Display | wwPDB validaton report |
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Full document | 4n19_full_validation.pdf.gz | 427.6 KB | Display | |
Data in XML | 4n19_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 4n19_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/4n19 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/4n19 | HTTPS FTP |
-Related structure data
Related structure data | 2ppnS 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: 11872.559 Da / Num. of mol.: 1 / Mutation: C22V, G89P 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 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.28 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→100 Å / Num. all: 23793 / Num. obs: 23793 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 48 |
Reflection shell | Resolution: 1.2→1.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.338 / % possible all: 6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2PPN Resolution: 1.2→10 Å / Occupancy max: 1 / Occupancy min: 0.1 / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 88.49 Å2 / Biso mean: 24.4197 Å2 / Biso min: 10.85 Å2 | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints | Type: s_bond_d / Dev ideal: 0.002 |