[English] 日本語
Yorodumi- PDB-3c4w: Crystal Structure of G protein coupled receptor kinase 1 bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of G protein coupled receptor kinase 1 bound to ATP and magnesium chloride at 2.7A | ||||||
Components | Rhodopsin kinase | ||||||
Keywords | TRANSFERASE / Ser/Thr kinase / RGS homology domain / G protein coupled receptor kinase / GRK / GRK1 / rhodopsin kinase / P-loop / phosphothreonine / autophosphorylation / amphipathic / ATP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Prenylation / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information rhodopsin kinase / rhodopsin kinase activity / regulation of opsin-mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein autophosphorylation / signal transduction / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Singh, P. / Tesmer, J.J.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structures of rhodopsin kinase in different ligand states reveal key elements involved in G protein-coupled receptor kinase activation. Authors: Singh, P. / Wang, B. / Maeda, T. / Palczewski, K. / Tesmer, J.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3c4w.cif.gz | 218.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3c4w.ent.gz | 173.5 KB | Display | PDB format |
PDBx/mmJSON format | 3c4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c4w_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3c4w_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3c4w_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 3c4w_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4w ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4w | HTTPS FTP |
-Related structure data
Related structure data | 3c4xC 3c4yC 3c4zC 3c50C 3c51C 2acxS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
|
-Components
#1: Protein | Mass: 61509.910 Da / Num. of mol.: 2 / Fragment: UNP residues 1-535 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Cell line (production host): High 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28327, rhodopsin kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.04 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.35 Details: PEG 3350, NaCl, glycerol, sodium tartarate, pH 4.35, ATP, magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97967 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97967 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 37248 / Redundancy: 6.8 % |
Reflection shell | Highest resolution: 2.7 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ACX Resolution: 2.7→19.98 Å / Cor.coef. Fo:Fc: 0.943 / SU B: 15.461 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.82 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.599 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|