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- PDB-4zk4: Crystal structure of a chimeric acetylcholine binding protein fro... -
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Basic information
Entry | Database: PDB / ID: 4zk4 | ||||||
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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 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane | ||||||
![]() | soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera | ||||||
![]() | ACETYLCHOLINE BINDING PROTEIN / AChBP / nicotinic / receptor / acetylcholine | ||||||
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, 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 7-(5- ...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 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane. Authors: Bobango, J. / Wu, J. / 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 | ![]() | 381.3 KB | Display | ![]() |
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PDB format | ![]() | 312.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1011.4 KB | Display | ![]() |
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Full document | ![]() | 1016.7 KB | Display | |
Data in XML | ![]() | 40.9 KB | Display | |
Data in CIF | ![]() | 58.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bynS ![]() 2bypS ![]() 2byrS ![]() 2bysS ![]() 2pgzS ![]() 3c79S ![]() 3c84S 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
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 26200.197 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: ![]() |
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-Non-polymers , 5 types, 449 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/TII.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/TII.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.7% PEG400, 0.085 M HEPES sodium, pH 7.5, 1.7 M ammonium sulfate, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 88 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 110948 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.09 Å2 / Rmerge(I) obs: 0.086 / Χ2: 2.82 / Net I/av σ(I): 40.746 / Net I/σ(I): 13.9 / Num. measured all: 812969 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84 Resolution: 1.901→49.135 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21.85 / 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: 98.51 Å2 / Biso mean: 32.2759 Å2 / Biso min: 11.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.901→49.135 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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