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- PDB-5tvc: Crystal structure of a chimeric acetylcholine binding protein fro... -
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Basic information
Entry | Database: PDB / ID: 5tvc | ||||||
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Title | Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine (TI-5312) | ||||||
![]() | Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera | ||||||
![]() | ACETYLCHOLINE-BINDING PROTEIN / nicotinic / acetylcholine / AChBP / chimeric protein | ||||||
Function / homology | ![]() regulation of acetylcholine secretion, neurotransmission / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / regulation of smooth muscle contraction / behavioral response to nicotine / acetylcholine receptor activity ...regulation of acetylcholine secretion, neurotransmission / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / regulation of smooth muscle contraction / behavioral response to nicotine / acetylcholine receptor activity / synaptic transmission, cholinergic / acetylcholine binding / acetylcholine receptor signaling pathway / activation of transmembrane receptor protein tyrosine kinase activity / acetylcholine-gated monoatomic cation-selective channel activity / regulation of dendrite morphogenesis / plasma membrane raft / membrane depolarization / ligand-gated monoatomic ion channel activity / monoatomic ion transport / excitatory postsynaptic potential / locomotory behavior / regulation of membrane potential / response to nicotine / nervous system development / postsynaptic membrane / postsynaptic density / nuclear speck / neuron projection / neuronal cell body / synapse / dendrite / Golgi apparatus / endoplasmic reticulum / signal transduction / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bobango, J. / Wu, J. / Talley, I.T. / Talley, T.T. | ||||||
![]() | ![]() Title: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with ...Title: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine (TI-5312) Authors: Bobango, J. / Wu, J. / Talley, I.T. / Talley, T.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222 KB | Display | ![]() |
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PDB format | ![]() | 175.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 43.5 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5syoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26315.285 Da / Num. of mol.: 5 Fragment: UNP residues 18-198 + 215-236 from Aplysia californica linked by loop C (UNP residues 215-230) from Homo sapiens Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: CHRNA3, NACHRA3 / Production host: ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-1PE / | #4: Chemical | ChemComp-7LB / ( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow | Temperature: 313 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→48.85 Å / Num. obs: 97444 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 27.58 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.253 / Net I/av σ(I): 33.629 / Net I/σ(I): 10.1 / Num. measured all: 733064 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _ / % possible all: 100
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5syo Resolution: 1.926→48.85 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.03 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.42 Å2 / Biso mean: 31.3635 Å2 / Biso min: 12.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.926→48.85 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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