[English] 日本語
![](img/lk-miru.gif)
- PDB-5afp: Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex w... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5afp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex with rhodopsin kinase peptide from Homo sapiens | |||||||||
![]() |
| |||||||||
![]() | SIGNALING PROTEIN | |||||||||
Function / homology | ![]() calcium-dependent protein kinase inhibitor activity / rhodopsin kinase / rhodopsin kinase activity / calcium sensitive guanylate cyclase activator activity / G protein-coupled receptor kinase activity / regulation of opsin-mediated signaling pathway / G protein-coupled opsin signaling pathway / regulation of presynaptic cytosolic calcium ion concentration / regulation of G protein-coupled receptor signaling pathway / presynaptic cytosol ...calcium-dependent protein kinase inhibitor activity / rhodopsin kinase / rhodopsin kinase activity / calcium sensitive guanylate cyclase activator activity / G protein-coupled receptor kinase activity / regulation of opsin-mediated signaling pathway / G protein-coupled opsin signaling pathway / regulation of presynaptic cytosolic calcium ion concentration / regulation of G protein-coupled receptor signaling pathway / presynaptic cytosol / regulation of synaptic vesicle exocytosis / postsynaptic cytosol / regulation of neuron projection development / positive regulation of exocytosis / calyx of Held / voltage-gated calcium channel activity / visual perception / positive regulation of calcium-mediated signaling / photoreceptor disc membrane / Inactivation, recovery and regulation of the phototransduction cascade / postsynapse / protein autophosphorylation / postsynaptic density / protein kinase activity / axon / glutamatergic synapse / dendrite / calcium ion binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Saleem, M. / Karuppiah, V. / Pandalaneni, S. / Burgoyne, R. / Derrick, J.P. / Lian, L.Y. | |||||||||
![]() | ![]() Title: Neuronal Calcium Sensor-1 Binds the D2 Dopamine Receptor and G-Protein Coupled Receptor Kinase 1 (Grk1) Peptides Using Different Modes of Interactions. Authors: Pandalaneni, S. / Karuppiah, V. / Saleem, M. / Haynes, L.P. / Burgoyne, R.D. / Mayans, O. / Derrick, J.P. / Lian, L.Y. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 161.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 128.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4yruC ![]() 5aeqC ![]() 5aerC ![]() 2you S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1), |
-
Components
#1: Protein | Mass: 21902.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 2550.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-25 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 0.12M ALCOHOLS (1,6-HEXANEDIOL; 1- BUTANOL;1,PROPANEDIOL(RACEMIC); 2-PROPONOL; 1, 4-BUTANEDIOL; 1,3- PROPANEDIOL); 0.1M BUFFER 2 (SODIUM HEPES; MOPS ACID PH 7.5); P550MME_P20K 30%. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Jul 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48 Å / Num. obs: 18488 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 94.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YOU ![]() 2you Resolution: 2.3→47.86 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.091 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.249 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.458 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|