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- PDB-1vry: Second and Third Transmembrane Domains of the Alpha-1 Subunit of ... -

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Entry
Database: PDB / ID: 1vry
TitleSecond and Third Transmembrane Domains of the Alpha-1 Subunit of Human Glycine Receptor
ComponentsGlycine receptor alpha-1 chain
KeywordsMEMBRANE PROTEIN / GLYCINE RECEPTOR / SECOND TRANSMEMBRANE DOMAIN / THIRD TRANSMEMBRANE DOMAIN
Function / homology
Function and homology information


taurine binding / response to alcohol / negative regulation of transmission of nerve impulse / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / positive regulation of acrosome reaction / neuromuscular process controlling posture / inhibitory synapse / righting reflex / regulation of respiratory gaseous exchange by nervous system process ...taurine binding / response to alcohol / negative regulation of transmission of nerve impulse / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / positive regulation of acrosome reaction / neuromuscular process controlling posture / inhibitory synapse / righting reflex / regulation of respiratory gaseous exchange by nervous system process / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic / glycinergic synapse / inhibitory postsynaptic potential / cellular response to ethanol / adult walking behavior / chloride transport / cellular response to zinc ion / glycine binding / startle response / chloride channel complex / neuronal action potential / neuropeptide signaling pathway / response to amino acid / monoatomic ion transport / chloride transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / regulation of membrane potential / visual perception / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / muscle contraction / 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 / membrane / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2810 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2810 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Helix non-globular / Special
Similarity search - Domain/homology
Glycine receptor subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMa, D. / Liu, Z. / Li, L. / Tang, P. / Xu, Y.
CitationJournal: Biochemistry / Year: 2005
Title: Structure and Dynamics of the Second and Third Transmembrane Domains of Human Glycine Receptor.
Authors: Ma, D. / Liu, Z. / Li, L. / Tang, P. / Xu, Y.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJul 26, 2005ID: 1ZHD
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / 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_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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)8,5301
Polymers8,5301
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50TARGET FUNCTION,STRUCTURES WITH THE LOWEST ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein Glycine receptor alpha-1 chain / Glycine receptor 48 kDa subunit / Strychnine binding subunit


Mass: 8530.070 Da / Num. of mol.: 1 / Fragment: SECOND AND THIRD TRANSMEMBRANE DOMAINS / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRA1 / Plasmid: PLYSS / 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
1113D 15N-SEPARATED NOESY
1212D NOESY
1312D TOCSY
1413D HNCA
1513D HNCO
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD 15N FILTERED NOESY SPECTROSCOPY AND H/D EXCHANGE EXPERIMENTS TOGETHER WITH HA AND CA CHEMICAL SHIFT INDEXES FOR IDENTIFICATION OF INTRAHELICAL HYDROGEN BONDING.

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Sample preparation

DetailsContents: 1MM TM23 U-15N, TRIFLUOROETHANOL-D2; 1MM TM23 U-15N,13C, TRIFLUOROETHANOL-D2
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.9.6SCHWIETERS, C.D. ET ALrefinement
XwinNMR2.6structure solution
NMRPIPE SGI6Xstructure solution
XPLOR-NIH2.9.6structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: TARGET FUNCTION,STRUCTURES WITH THE LOWEST ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS
Conformers calculated total number: 50 / Conformers submitted total number: 20

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