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Yorodumi- PDB-3jwr: Crystal structure of chimeric PDE5/PDE6 catalytic domain complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jwr | ||||||
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Title | Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (IBMX) and PDE6 gamma-subunit inhibitory peptide 70-87. | ||||||
Components |
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Keywords | HYDROLASE / mostly alpha / cGMP / Polymorphism / Sensory transduction / Vision | ||||||
Function / homology | Function and homology information Wnt signaling pathway, calcium modulating pathway / : / positive regulation of oocyte development / regulation of opsin-mediated signaling pathway / retinal cone cell development / 3',5'-cyclic-GMP phosphodiesterase / G protein-coupled opsin signaling pathway / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / positive regulation of G protein-coupled receptor signaling pathway ...Wnt signaling pathway, calcium modulating pathway / : / positive regulation of oocyte development / regulation of opsin-mediated signaling pathway / retinal cone cell development / 3',5'-cyclic-GMP phosphodiesterase / G protein-coupled opsin signaling pathway / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / positive regulation of G protein-coupled receptor signaling pathway / phototransduction, visible light / oocyte development / enzyme inhibitor activity / relaxation of cardiac muscle / RHOBTB1 GTPase cycle / positive regulation of epidermal growth factor receptor signaling pathway / photoreceptor outer segment membrane / spectrin binding / positive regulation of cardiac muscle hypertrophy / cGMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / Smooth Muscle Contraction / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / negative regulation of T cell proliferation / T cell proliferation / visual perception / cAMP-mediated signaling / Activation of the phototransduction cascade / photoreceptor disc membrane / Inactivation, recovery and regulation of the phototransduction cascade / Ca2+ pathway / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å | ||||||
Authors | Barren, B. / Gakhar, L. / Muradov, H. / Boyd, K.K. / Ramaswamy, S. / Artemyev, N.O. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit Authors: Barren, B. / Gakhar, L. / Muradov, H. / Boyd, K.K. / Ramaswamy, S. / Artemyev, N.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jwr.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jwr.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 3jwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jwr_validation.pdf.gz | 469.6 KB | Display | wwPDB validaton report |
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Full document | 3jwr_full_validation.pdf.gz | 493.5 KB | Display | |
Data in XML | 3jwr_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 3jwr_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/3jwr ftp://data.pdbj.org/pub/pdb/validation_reports/jw/3jwr | HTTPS FTP |
-Related structure data
Related structure data | 3jwqSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 38282.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: O76074, UniProt: P51160, 3',5'-cyclic-GMP phosphodiesterase #2: Protein/peptide | Mass: 2185.436 Da / Num. of mol.: 2 / Fragment: sequence database residues 70-87 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) References: UniProt: P18545, 3',5'-cyclic-nucleotide phosphodiesterase |
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-Non-polymers , 4 types, 26 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IBM / #6: 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: 2.83 Å3/Da / Density % sol: 56.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM HEPES, 1 M sodium citrate, 2.5% ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0332 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Nov 24, 2008 |
Radiation | Monochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→40.41 Å / Num. all: 17916 / Num. obs: 17916 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.99→3.1 Å / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3JWQ Resolution: 2.994→40.413 Å / SU ML: 0.47 / σ(F): 1.61 / Phase error: 26.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.694 Å2 / ksol: 0.321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.994→40.413 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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