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Yorodumi- PDB-3g4g: Crystal structure of human phosphodiesterase 4d with regulatory d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g4g | ||||||
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Title | Crystal structure of human phosphodiesterase 4d with regulatory domain and d155871 | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | ||||||
Keywords | HYDROLASE / phosphodiesterase / PDE4D / UCR2 / Alternative splicing / cAMP / Cytoplasm / Cytoskeleton / Membrane / Metal-binding / Phosphoprotein | ||||||
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 / regulation of cardiac muscle cell contraction / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / beta-2 adrenergic receptor binding / 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 / regulation of cardiac muscle cell contraction / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / beta-2 adrenergic receptor binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / heterocyclic compound binding / adrenergic receptor signaling pathway / voltage-gated calcium channel complex / regulation of cell communication by electrical coupling involved in cardiac conduction / cAMP catabolic process / calcium channel regulator activity / cAMP-mediated signaling / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / DARPP-32 events / negative regulation of peptidyl-serine phosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cAMP binding / cellular response to cAMP / cellular response to epinephrine stimulus / calcium channel complex / positive regulation of interleukin-2 production / regulation of heart rate / positive regulation of type II interferon production / ATPase binding / T cell receptor signaling pathway / G alpha (s) signalling events / scaffold protein binding / transmembrane transporter binding / apical plasma membrane / centrosome / perinuclear region of cytoplasm / enzyme binding / signal transduction / membrane / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Staker, B.L. | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2010 Title: Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety. Authors: Burgin, A.B. / Magnusson, O.T. / Singh, J. / Witte, P. / Staker, B.L. / Bjornsson, J.M. / Thorsteinsdottir, M. / Hrafnsdottir, S. / Hagen, T. / Kiselyov, A.S. / Stewart, L.J. / Gurney, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g4g.cif.gz | 285 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g4g.ent.gz | 228.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/3g4g ftp://data.pdbj.org/pub/pdb/validation_reports/g4/3g4g | HTTPS FTP |
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-Related structure data
Related structure data | 3g45C 3g4iC 3g4kC 3g4lC 3g58C 3iadC 3gpz C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Details | Authors state that the BIOLOGICAL UNIT IS UNKNOWN. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 48370.801 Da / Num. of mol.: 4 / Fragment: residues 299-347 and 360-714 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4D, DPDE3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q08499, 3',5'-cyclic-nucleotide phosphodiesterase |
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-Non-polymers , 5 types, 183 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-D71 / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THE LINKER REGION IS FROM PDE4C THAT WAS SWAPPED TO REPLACE THE NATURAL LINKER, ...AUTHORS STATE THAT THE LINKER REGION IS FROM PDE4C THAT WAS SWAPPED TO REPLACE THE NATURAL LINKER, AS THE NATURAL LINKER WAS HIGHLY CHARGED. |
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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 Å3/Da / Density % sol: 38.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 100MM HEPES PH 7.5, 100 MM NACL, 18% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 64589 / % possible obs: 95 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.391 / % possible all: 74.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.8 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.299 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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