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Yorodumi- PDB-5afp: Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5afp | |||||||||
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Title | Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex with rhodopsin kinase peptide from Homo sapiens | |||||||||
Components |
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Keywords | SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information 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 / postsynaptic cytosol / regulation of neuron projection development / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / calyx of Held / voltage-gated calcium channel activity / positive regulation of calcium-mediated signaling / visual perception / photoreceptor disc membrane / Inactivation, recovery and regulation of the phototransduction cascade / postsynapse / protein autophosphorylation / postsynaptic density / protein kinase activity / axon / glutamatergic synapse / calcium ion binding / dendrite / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Saleem, M. / Karuppiah, V. / Pandalaneni, S. / Burgoyne, R. / Derrick, J.P. / Lian, L.Y. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5afp.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5afp.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 5afp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5afp_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 5afp_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 5afp_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 5afp_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/5afp ftp://data.pdbj.org/pub/pdb/validation_reports/af/5afp | HTTPS FTP |
-Related structure data
Related structure data | 4yruC 5aeqC 5aerC 2you 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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1 |
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2 |
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Unit cell |
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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.) RATTUS NORVEGICUS (Norway rat) / Cell: NEURON / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62168 #2: Protein/peptide | Mass: 2550.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-25 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15835 #3: Chemical | ChemComp-CA / #4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9 |
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
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
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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: 46.458 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→47.86 Å
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