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- PDB-2ksr: NMR structures of TM domain of the n-Acetylcholine receptor b2 subunit -

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Basic information

Entry
Database: PDB / ID: 2ksr
TitleNMR structures of TM domain of the n-Acetylcholine receptor b2 subunit
ComponentsNeuronal acetylcholine receptor subunit beta-2
KeywordsMEMBRANE PROTEIN / nicotinic acetylcholine receptors / transmembrane domain / HFIP / Cell junction / Cell membrane / Disease mutation / Disulfide bond / 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
Neurotransmitter-gated ion-channel transmembrane domain / 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 transmembrane domain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Neuronal acetylcholine receptor subunit beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsBondarenko, V. / Tillman, T. / Xu, Y. / Tang, P.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: NMR structure of the transmembrane domain of the n-acetylcholine receptor beta2 subunit.
Authors: Bondarenko, V. / Tillman, T. / Xu, Y. / Tang, P.
History
DepositionJan 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuronal acetylcholine receptor subunit beta-2


Theoretical massNumber of molelcules
Total (without water)18,4741
Polymers18,4741
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 Neuronal acetylcholine receptor subunit beta-2


Mass: 18474.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNB2 / Plasmid: pTBSG1 / Production host: Escherichia coli (E. coli) / 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-13C HSQC
1313D HN(CO)CA
1413D HNCA
1513D HNCO
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1812D 1H-1H NOESY
1913D CBCA(CO)NH
11022D 1H-15N HSQC
11122D 1H-13C HSQC
11223D HNCA
11323D 1H-15N NOESY
11423D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-100% 13C; U-100% 15N] TM123, 50% HFIP/50% H2O50% HFIP/50% H2O
20.2 mM [U-100% 13C; U-100% 15N] TM1234, 50% HFIP/ 50% H2O50% HFIP/ 50% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMTM123[U-100% 13C; U-100% 15N]1
0.2 mMTM1234[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0 / pH: 3.8 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, P. et al.structure solution
CYANA2.1Guntert, P. et al.chemical shift assignment
CYANA2.1Guntert, P. et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1454 / NOE intraresidue total count: 524 / NOE long range total count: 27 / NOE medium range total count: 389 / NOE sequential total count: 514
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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