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- PDB-1mot: NMR Structure Of Extended Second Transmembrane Domain Of Glycine ... -

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Basic information

Entry
Database: PDB / ID: 1mot
TitleNMR Structure Of Extended Second Transmembrane Domain Of Glycine Receptor alpha1 Subunit in SDS Micelles
ComponentsGlycine Receptor alpha-1 CHAIN
KeywordsMEMBRANE PROTEIN / glycine receptor / second transmembrane domain / micelles
Function / homology
Function and homology information


taurine binding / negative regulation of transmission of nerve impulse / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / positive regulation of acrosome reaction / synaptic transmission, glycinergic / neuromuscular process controlling posture / inhibitory synapse / regulation of respiratory gaseous exchange by nervous system process / righting reflex ...taurine binding / negative regulation of transmission of nerve impulse / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / positive regulation of acrosome reaction / synaptic transmission, glycinergic / neuromuscular process controlling posture / inhibitory synapse / regulation of respiratory gaseous exchange by nervous system process / righting reflex / extracellularly glycine-gated chloride channel activity / response to alcohol / glycinergic synapse / inhibitory postsynaptic potential / cellular response to ethanol / chloride transport / adult walking behavior / cellular response to zinc ion / neurotransmitter receptor activity / glycine binding / startle response / chloride channel complex / neuronal action potential / neuropeptide signaling pathway / transmembrane transporter complex / monoatomic ion transport / chloride transmembrane transport / muscle contraction / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / visual perception / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / transmembrane signaling receptor activity / perikaryon / postsynaptic membrane / neuron projection / external side of plasma membrane / intracellular membrane-bounded organelle / neuronal cell body / dendrite / synapse / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Glycine receptor alpha1 / Glycine receptor alpha / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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 ...Glycine receptor alpha1 / Glycine receptor alpha / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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
Glycine receptor subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsYushmanov, V.E. / Mandal, P.K. / Liu, Z. / Tang, P. / Xu, Y.
CitationJournal: Biochemistry / Year: 2003
Title: NMR Structure and Backbone Dynamics of the Extended Second Transmembrane Domain of the Human Neuronal Glycine Receptor Alpha1 Subunit
Authors: Yushmanov, V.E. / Mandal, P.K. / Liu, Z. / Tang, P. / Xu, Y.
History
DepositionSep 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 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: Glycine Receptor alpha-1 CHAIN


Theoretical massNumber of molelcules
Total (without water)2,8041
Polymers2,8041
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 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Glycine Receptor alpha-1 CHAIN / Glycine Receptor alpha1 subunit / Glycine Receptor 48KDA SUBUNIT / STRYCHNINE BINDING SUBUNIT


Mass: 2804.249 Da / Num. of mol.: 1 / Fragment: Extented second transmembrane domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRA1 / Plasmid: pGEX-3X / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P23415

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
141COSY
15115N T1
16115N T2
17115N Het-NOE
NMR detailsText: The structure was determined using standard 2D homonuclear and triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: SDS concentration: 300 mM Peptide concentration: 2 mM
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 300 mM SDS concentration / pH: 5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.T.structure solution
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 187 restraints, 169 are NOE-derived distance constraints,18 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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