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- PDB-2lly: NMR structures of the transmembrane domains of the nAChR a4 subunit -

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Basic information

Entry
Database: PDB / ID: 2lly
TitleNMR structures of the transmembrane domains of the nAChR a4 subunit
ComponentsNeuronal acetylcholine receptor subunit alpha-4
KeywordsTRANSPORT PROTEIN / Acetylcholine receptor / Transmembrane domain
Function / homology
Function and homology information


Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / behavioral response to nicotine / acetylcholine-gated monoatomic cation-selective channel activity / inhibitory postsynaptic potential / nervous system process / acetylcholine binding ...Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / behavioral response to nicotine / acetylcholine-gated monoatomic cation-selective channel activity / inhibitory postsynaptic potential / nervous system process / acetylcholine binding / synaptic transmission, cholinergic / acetylcholine receptor signaling pathway / regulation of dopamine secretion / action potential / B cell activation / membrane depolarization / ligand-gated monoatomic ion channel activity / monoatomic ion transport / sensory perception of pain / regulation of membrane potential / response to nicotine / cognition / calcium ion transport / chemical synaptic transmission / postsynaptic membrane / response to oxidative stress / response to hypoxia / neuron projection / external side of plasma membrane / DNA repair / neuronal cell body / dendrite / synapse / 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 alpha-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 11
AuthorsBondarenko, V. / Mowrey, D. / Tillman, T. / Cui, T. / Liu, L.T. / Xu, Y. / Tang, P.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: NMR structures of the transmembrane domains of the a4b2 nAChR.
Authors: Bondarenko, V. / Mowrey, D. / Tillman, T. / Cui, T. / Liu, L.T. / Xu, Y. / Tang, P.
History
DepositionNov 18, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuronal acetylcholine receptor subunit alpha-4


Theoretical massNumber of molelcules
Total (without water)15,0211
Polymers15,0211
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 #1closest to the average

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Components

#1: Protein Neuronal acetylcholine receptor subunit alpha-4


Mass: 15020.915 Da / Num. of mol.: 1
Fragment: Helical transmembrane region, residues 242-339 and residues 598-625
Mutation: R240E, R241E, L301S, I303S, L305S, R336E, M626E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA4, NACRA4 / Production host: Escherichia coli (E. coli) / References: UniProt: P43681

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HNCO
1712D 1H-15N HSQC
1812D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.25 mM [U-100% 13C; U-100% 15N] protein, 5 mM sodium acetate, 1.5 % LDAO, 10 mM sodium chloride, 5 % [U-100% 2H] D2O, 0.1 mM DSS, 10 mM sodium chloride, 20 mM beta-mercaptoethanol, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMentity-1[U-100% 13C; U-100% 15N]1
5 mMsodium acetate-21
1.5 %LDAO-31
10 mMsodium chloride-41
5 %D2O-5[U-100% 2H]1
0.1 mMDSS-61
10 mMsodium chloride-71
20 mMbeta-mercaptoethanol-81
Sample conditionspH: 4.65 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1070 / NOE intraresidue total count: 362 / NOE long range total count: 28 / NOE medium range total count: 259 / NOE sequential total count: 421 / Hydrogen bond constraints total count: 296 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 90 / Protein psi angle constraints total count: 90
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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