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Yorodumi- PDB-5aer: Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex w... -
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-Basic information
Entry | Database: PDB / ID: 5aer | |||||||||
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Title | Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex with D2 dopamine receptor peptide from Homo sapiens | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / NEURONAL CALCIUM SENSOR-1 / DOPAMINE RECEPTOR 2 | |||||||||
Function / homology | Function and homology information regulation of locomotion involved in locomotory behavior / negative regulation of dopamine receptor signaling pathway / calcium-dependent protein kinase inhibitor activity / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of circadian sleep/wake cycle, sleep / acid secretion / positive regulation of glial cell-derived neurotrophic factor production / dopamine neurotransmitter receptor activity, coupled via Gi/Go / auditory behavior / nervous system process involved in regulation of systemic arterial blood pressure ...regulation of locomotion involved in locomotory behavior / negative regulation of dopamine receptor signaling pathway / calcium-dependent protein kinase inhibitor activity / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of circadian sleep/wake cycle, sleep / acid secretion / positive regulation of glial cell-derived neurotrophic factor production / dopamine neurotransmitter receptor activity, coupled via Gi/Go / auditory behavior / nervous system process involved in regulation of systemic arterial blood pressure / regulation of synapse structural plasticity / calcium sensitive guanylate cyclase activator activity / response to histamine / positive regulation of renal sodium excretion / adenohypophysis development / neuron-neuron synaptic transmission / hyaloid vascular plexus regression / cerebral cortex GABAergic interneuron migration / regulation of potassium ion transport / negative regulation of neuron migration / Dopamine receptors / adenylate cyclase-inhibiting dopamine receptor signaling pathway / negative regulation of cellular response to hypoxia / orbitofrontal cortex development / response to inactivity / dopamine binding / regulation of dopamine uptake involved in synaptic transmission / branching morphogenesis of a nerve / negative regulation of voltage-gated calcium channel activity / negative regulation of dopamine secretion / positive regulation of growth hormone secretion / heterotrimeric G-protein binding / regulation of presynaptic cytosolic calcium ion concentration / behavioral response to ethanol / dopaminergic synapse / drinking behavior / peristalsis / G protein-coupled receptor complex / phospholipase C-activating dopamine receptor signaling pathway / grooming behavior / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of urine volume / striatum development / negative regulation of adenylate cyclase activity / positive regulation of multicellular organism growth / negative regulation of synaptic transmission, glutamatergic / presynaptic cytosol / G protein-coupled receptor internalization / non-motile cilium / response to morphine / adult walking behavior / response to iron ion / ciliary membrane / postsynaptic cytosol / regulation of neuron projection development / regulation of synaptic transmission, GABAergic / dopamine uptake involved in synaptic transmission / arachidonic acid secretion / temperature homeostasis / regulation of synaptic vesicle exocytosis / pigmentation / postsynaptic modulation of chemical synaptic transmission / heterocyclic compound binding / dopamine metabolic process / positive regulation of neuroblast proliferation / negative regulation of cytosolic calcium ion concentration / regulation of dopamine secretion / positive regulation of cytokinesis / positive regulation of exocytosis / associative learning / calyx of Held / positive regulation of receptor internalization / behavioral response to cocaine / endocytic vesicle / lateral plasma membrane / G-protein alpha-subunit binding / neuroblast proliferation / response to axon injury / response to light stimulus / voltage-gated calcium channel activity / GABA-ergic synapse / potassium channel regulator activity / sperm flagellum / negative regulation of protein secretion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of insulin secretion / prepulse inhibition / long-term memory / positive regulation of calcium-mediated signaling / axon terminus / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / release of sequestered calcium ion into cytosol / synapse assembly / response to amphetamine / presynaptic modulation of chemical synaptic transmission / negative regulation of blood pressure / negative regulation of innate immune response / excitatory postsynaptic potential / regulation of heart rate Similarity search - Function | |||||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aer.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aer.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 5aer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aer_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 5aer_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 5aer_validation.xml.gz | 10 KB | Display | |
Data in CIF | 5aer_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aer ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aer | HTTPS FTP |
-Related structure data
Related structure data | 4yruC 5aeqC 5afpC 1g8iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.58, -0.75, 0.3), Vector: |
-Components
#1: Protein | Mass: 21902.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Tissue: NEURON / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62168 | ||||||
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#2: Protein/peptide | Mass: 1720.066 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P14416 #3: Chemical | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 |
Detector | Type: MARRESEARCH MARMOSAIC 300MM / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→51 Å / Num. obs: 11235 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.19→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 77.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G8I Resolution: 2.19→51.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.902 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.247 / 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: 40.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→51.38 Å
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