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- PDB-2m6b: Structure of full-length transmembrane domains of human glycine r... -

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Basic information

Entry
Database: PDB / ID: 2m6b
TitleStructure of full-length transmembrane domains of human glycine receptor alpha1 monomer subunit
ComponentsFull-Length Transmembrane Domains of Human Glycine Receptor alpha1 Subunit
KeywordsMEMBRANE PROTEIN / glycine receptor / anion channel / 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
Glycine receptor alpha1 / Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / 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 ...Glycine receptor alpha1 / Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Glycine receptor subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMowrey, D. / Cui, T. / Jia, Y. / Ma, D. / Makhov, A.M. / Zhang, P. / Tang, P. / Xu, Y.
CitationJournal: Structure / Year: 2013
Title: Open-Channel Structures of the Human Glycine Receptor alpha 1 Full-Length Transmembrane Domain.
Authors: Mowrey, D.D. / Cui, T. / Jia, Y. / Ma, D. / Makhov, A.M. / Zhang, P. / Tang, P. / Xu, Y.
History
DepositionMar 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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
Revision 1.4May 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: Full-Length Transmembrane Domains of Human Glycine Receptor alpha1 Subunit


Theoretical massNumber of molelcules
Total (without water)17,3201
Polymers17,3201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Full-Length Transmembrane Domains of Human Glycine Receptor alpha1 Subunit


Mass: 17320.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-31b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P23415*PLUS

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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 HNCO
1413D HNCA
1513D HN(CO)CA
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-15N NOESY
11113D 1H-15N NOESY
11213D 1H-15N NOESY
11313D 1H-15N NOESY

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Sample preparation

DetailsContents: 280 uM protein, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 280 uM / Component: protein-1
Sample conditionspH: 5.8 / Pressure: ambient / Temperature: 313 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 softwareName: CYANA / Version: 3 / Developer: Guntert, P. et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1014 / NOE intraresidue total count: 321 / NOE long range total count: 21 / NOE medium range total count: 324 / NOE sequential total count: 348 / Hydrogen bond constraints total count: 212 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 219 / Protein phi angle constraints total count: 76 / Protein psi angle constraints total count: 76
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0.13 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 15 / Maximum torsion angle constraint violation: 1.29 ° / Maximum upper distance constraint violation: 0.24 Å

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