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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
TitleCrystal 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)
ComponentsSoluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera
KeywordsACETYLCHOLINE-BINDING PROTEIN / nicotinic / acetylcholine / AChBP / chimeric protein
Function / homology
Function and homology information


regulation of acetylcholine secretion, neurotransmission / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / synaptic transmission involved in micturition / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of smooth muscle contraction / behavioral response to nicotine ...regulation of acetylcholine secretion, neurotransmission / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / synaptic transmission involved in micturition / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of smooth muscle contraction / behavioral response to nicotine / neuromuscular synaptic transmission / acetylcholine-gated monoatomic cation-selective channel activity / cation channel complex / acetylcholine binding / synaptic transmission, cholinergic / acetylcholine receptor signaling pathway / neurotransmitter receptor complex / ligand-gated monoatomic ion channel activity / regulation of dendrite morphogenesis / plasma membrane raft / membrane depolarization / extracellular ligand-gated monoatomic ion channel activity / monoatomic ion transport / response to nicotine / regulation of membrane potential / excitatory postsynaptic potential / locomotory behavior / transmembrane signaling receptor activity / nervous system development / monoatomic ion transmembrane transport / postsynaptic membrane / neuron projection / nuclear speck / ciliary basal body / neuronal cell body / intracellular membrane-bounded organelle / dendrite / synapse / nucleolus / endoplasmic reticulum / Golgi apparatus / signal transduction / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel ...Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-7LB / Neuronal acetylcholine receptor subunit alpha-3 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.926 Å
AuthorsBobango, J. / Wu, J. / Talley, I.T. / Talley, T.T.
CitationJournal: To Be Published
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
DepositionNov 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera
B: Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera
C: Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera
D: Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera
E: Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,46416
Polymers131,5765
Non-polymers1,88811
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15450 Å2
ΔGint-136 kcal/mol
Surface area40760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.854, 78.040, 120.569
Angle α, β, γ (deg.)90.000, 95.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Soluble acetylcholine receptor,Neuronal acetylcholine receptor subunit alpha-3 chimera


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.) Aplysia californica (California sea hare), (gene. exp.) Homo sapiens (human)
Gene: CHRNA3, NACHRA3 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8, UniProt: P32297
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-7LB / (E,2S)-N-methyl-5-(5-phenoxy-3-pyridyl)pent-4-en-2-amine / (2S,4E)-N-methyl-5-(5-phenoxypyridin-3-yl)pent-4-en-2-amine


Mass: 268.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H20N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2
1.93-1.967.50.54948530.696
1.96-27.60.48548580.72
2-2.047.60.3848250.733
2.04-2.087.60.33548480.766
2.08-2.127.60.29148690.773
2.12-2.177.60.25348320.817
2.17-2.237.60.23148470.843
2.23-2.297.60.19748680.864
2.29-2.367.60.17148450.89
2.36-2.437.60.1548440.932
2.43-2.527.60.14348660.972
2.52-2.627.60.12148671.008
2.62-2.747.60.10448411.084
2.74-2.887.60.08848851.188
2.88-3.067.60.07648891.419
3.06-3.37.60.06948582.006
3.3-3.637.30.06548992.74
3.63-4.167.20.05948913.024
4.16-5.247.20.04449282.21
5.24-507.50.03450311.548

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11rc3_2545refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5syo

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
RfactorNum. reflection% reflection
Rfree0.225 4870 5 %
Rwork0.1886 92532 -
obs0.1904 97402 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.42 Å2 / Biso mean: 31.3635 Å2 / Biso min: 12.49 Å2
Refinement stepCycle: final / Resolution: 1.926→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7867 0 126 478 8471
Biso mean--39.23 33.14 -
Num. residues----1020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118209
X-RAY DIFFRACTIONf_angle_d1.16211232
X-RAY DIFFRACTIONf_chiral_restr0.0681273
X-RAY DIFFRACTIONf_plane_restr0.0081428
X-RAY DIFFRACTIONf_dihedral_angle_d10.2034804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9264-1.94830.25451610.21462847300891
1.9483-1.97120.23571460.202430563202100
1.9712-1.99530.28211510.202131283279100
1.9953-2.02050.25761640.1930213185100
2.0205-2.04710.23931590.190931083267100
2.0471-2.07510.24491810.185230433224100
2.0751-2.10480.2271600.188330903250100
2.1048-2.13620.26251410.187730863227100
2.1362-2.16960.21941660.184830663232100
2.1696-2.20520.23241630.18530423205100
2.2052-2.24320.23871810.192131033284100
2.2432-2.2840.23711570.181730953252100
2.284-2.32790.21031830.184930663249100
2.3279-2.37540.23881770.172930653242100
2.3754-2.42710.22131600.175130693229100
2.4271-2.48350.18921690.178830913260100
2.4835-2.54560.22331490.19130863235100
2.5456-2.61450.27671460.192331083254100
2.6145-2.69140.26471800.201630783258100
2.6914-2.77820.24851610.197430933254100
2.7782-2.87750.22791700.191530813251100
2.8775-2.99270.25071750.198930973272100
2.9927-3.12890.25321840.198330453229100
3.1289-3.29380.21761490.196631253274100
3.2938-3.50010.20291490.189631293278100
3.5001-3.77030.23561740.19130803254100
3.7703-4.14950.19771380.164731403278100
4.1495-4.74960.17721570.157931253282100
4.7496-5.98220.19851540.175931573311100
5.9822-48.86550.23461650.235232123377100

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