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- PDB-2k59: NMR structures of the second transmembrane domain of the neuronal... -

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Entry
Database: PDB / ID: 2k59
TitleNMR structures of the second transmembrane domain of the neuronal acetylcholine receptor beta 2 subunit
ComponentsNeuronal acetylcholine receptor subunit beta-2
KeywordsTRANSPORT PROTEIN / neuronal acetylcholine receptor / second transmembrane domain / beta 2 subunit / Cell junction / Disease mutation / Epilepsy / Glycoprotein / Ion transport / Ionic channel / Membrane / Polymorphism / Postsynaptic cell membrane / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


vestibulocochlear nerve development / lateral geniculate nucleus development / regulation of circadian sleep/wake cycle, REM sleep / regulation of synaptic transmission, dopaminergic / quaternary ammonium group binding / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / optic nerve morphogenesis / response to acetylcholine ...vestibulocochlear nerve development / lateral geniculate nucleus development / regulation of circadian sleep/wake cycle, REM sleep / regulation of synaptic transmission, dopaminergic / quaternary ammonium group binding / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / optic nerve morphogenesis / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / central nervous system projection neuron axonogenesis / acetylcholine-gated channel complex / cholinergic synapse / regulation of dopamine metabolic process / negative regulation of action potential / behavioral response to nicotine / positive regulation of dopamine secretion / acetylcholine receptor activity / synaptic transmission, cholinergic / acetylcholine binding / postsynaptic specialization membrane / nervous system process / acetylcholine receptor signaling pathway / acetylcholine-gated monoatomic cation-selective channel activity / regulation of synapse assembly / regulation of dendrite morphogenesis / heterocyclic compound binding / B cell activation / regulation of dopamine secretion / plasma membrane raft / membrane depolarization / associative learning / social behavior / ligand-gated monoatomic ion channel activity / smooth muscle contraction / monoatomic ion transport / positive regulation of B cell proliferation / sensory perception of pain / visual perception / response to cocaine / learning / locomotory behavior / sensory perception of sound / response to nicotine / visual learning / memory / cognition / calcium ion transport / presynaptic membrane / response to ethanol / response to hypoxia / neuron projection / external side of plasma membrane / synapse / protein-containing complex binding / signal transduction / membrane / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / 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
Similarity search - Domain/homology
Neuronal acetylcholine receptor subunit beta-2
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsBondarenko, V. / Tang, P. / Xu, Y. / Yushmanov, V.
CitationJournal: Biochemistry / Year: 2003
Title: NMR structure and dynamics of the second transmembrane domain of the neuronal acetylcholine receptor beta 2 subunit
Authors: Yushmanov, V.E. / Xu, Y. / Tang, P.
History
DepositionJun 25, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
B: Neuronal acetylcholine receptor subunit beta-2


Theoretical massNumber of molelcules
Total (without water)3,0461
Polymers3,0461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Neuronal acetylcholine receptor subunit beta-2


Mass: 3045.824 Da / Num. of mol.: 1 / Fragment: UNP residues 264-291 / Source method: obtained synthetically / Details: solid-phase synthesis / References: UniProt: P17787

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 3-5 mM [U-100% 15N] nAChR TM2, 0.5 mM DSS, 450-750 mM DPC, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mMnAChR TM2[U-100% 15N]1
0.5 mMDSS1
600 mMDPC1
Sample conditionsIonic strength: 0.25 / pH: 5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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