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Yorodumi- PDB-6akr: Crystal structure of the PDE4D catalytic domain in complex with o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6akr | |||||||||||||||
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Title | Crystal structure of the PDE4D catalytic domain in complex with osthole | |||||||||||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | |||||||||||||||
Keywords | HYDROLASE / phosphodiesterase 4d | |||||||||||||||
Function / homology | Function and homology information signaling receptor regulator activity / negative regulation of relaxation of cardiac muscle / negative regulation of heart contraction / 3',5'-cyclic-AMP phosphodiesterase / positive regulation of interleukin-5 production / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / establishment of endothelial barrier / regulation of cardiac muscle cell contraction / negative regulation of cAMP-mediated signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel ...signaling receptor regulator activity / negative regulation of relaxation of cardiac muscle / negative regulation of heart contraction / 3',5'-cyclic-AMP phosphodiesterase / positive regulation of interleukin-5 production / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / establishment of endothelial barrier / regulation of cardiac muscle cell contraction / negative regulation of cAMP-mediated signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / positive regulation of heart rate / heterocyclic compound binding / adrenergic receptor signaling pathway / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-serine phosphorylation / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / DARPP-32 events / calcium channel regulator activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / beta-2 adrenergic receptor binding / cAMP binding / cellular response to cAMP / calcium channel complex / cellular response to epinephrine stimulus / positive regulation of interleukin-2 production / regulation of heart rate / cAMP-mediated signaling / positive regulation of type II interferon production / T cell receptor signaling pathway / ATPase binding / scaffold protein binding / G alpha (s) signalling events / transmembrane transporter binding / apical plasma membrane / centrosome / perinuclear region of cytoplasm / enzyme binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.326 Å | |||||||||||||||
Authors | Wang, S. / Huo, Y.W. / Xie, Y. | |||||||||||||||
Funding support | United States, China, 4items
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Citation | Journal: Sci.Signal. / Year: 2020 Title: Airway relaxation mechanisms and structural basis of osthole for improving lung function in asthma. Authors: Wang, S. / Xie, Y. / Huo, Y.W. / Li, Y. / Abel, P.W. / Jiang, H. / Zou, X. / Jiao, H.Z. / Kuang, X. / Wolff, D.W. / Huang, Y.G. / Casale, T.B. / Panettieri Jr., R.A. / Wei, T. / Cao, Z. / Tu, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6akr.cif.gz | 282.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6akr.ent.gz | 226.3 KB | Display | PDB format |
PDBx/mmJSON format | 6akr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6akr_validation.pdf.gz | 5 MB | Display | wwPDB validaton report |
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Full document | 6akr_full_validation.pdf.gz | 5.1 MB | Display | |
Data in XML | 6akr_validation.xml.gz | 53.3 KB | Display | |
Data in CIF | 6akr_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6akr ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6akr | HTTPS FTP |
-Related structure data
Related structure data | 1q9mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 41808.242 Da / Num. of mol.: 4 / Fragment: UNP residues 381-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4D / Production host: Escherichia coli (E. coli) References: UniProt: Q08499, 3',5'-cyclic-AMP phosphodiesterase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-A0O / #4: Water | ChemComp-HOH / | |
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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: 2.93 Å3/Da / Density % sol: 58.02 % |
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Crystal grow | Temperature: 277.15 K / Method: evaporation Details: 0.1M HEPES, 18% PEG3350, 25% ethylene glycol, 10% isopropanol, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 76639 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.44 / Num. unique obs: 7464 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q9M Resolution: 2.326→48.643 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.326→48.643 Å
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Refine LS restraints |
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LS refinement shell |
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