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- PDB-1dxz: M2 TRANSMEMBRANE SEGMENT OF ALPHA-SUBUNIT OF NICOTINIC ACETYLCHOL... -

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Basic information

Entry
Database: PDB / ID: 1dxz
TitleM2 TRANSMEMBRANE SEGMENT OF ALPHA-SUBUNIT OF NICOTINIC ACETYLCHOLINE RECEPTOR FROM TORPEDO CALIFORNICA, NMR, 20 STRUCTURES
ComponentsACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN
KeywordsTRANSMEMBRANE PROTEIN / NICOTINIC ACETYLCHOLINE RECEPTOR / TRANSMEMBRANE SEGMENT / M2 / ION-CHANNEL
Function / homology
Function and homology information


acetylcholine-gated monoatomic cation-selective channel activity / transmembrane signaling receptor activity / postsynaptic membrane / neuron projection
Similarity search - Function
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
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodSOLUTION NMR / distance geometry
AuthorsPashkov, V.S. / Maslennikov, I.V. / Tchikin, L.D. / Efremov, R.G. / Ivanov, V.T. / Arseniev, A.S.
CitationJournal: FEBS Lett. / Year: 1999
Title: Spatial Structure of the M2 Transmembrane Segment of the Nicotinic Acetylcholine Receptor Alpha-Subunit
Authors: Pashkov, V.S. / Maslennikov, I.V. / Tchikin, L.D. / Efremov, R.G. / Ivanov, V.T. / Arseniev, A.S.
History
DepositionJan 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)3,4161
Polymers3,4161
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 / 300LEAST RESTRAINTS VIOLATION
RepresentativeModel #4

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Components

#1: Protein/peptide ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN


Mass: 3416.075 Da / Num. of mol.: 1 / Fragment: M2 TRANSMEMBRANE SEGMENT / Source method: obtained synthetically
Details: THE C-TERMINAL RESIDUE OF THE PEPTIDE IS AMIDATED. THE COMPLETE RECEPTOR CONSISTS OF A PENTAMER OF TWO ALPHA CHAINS, AND ONE EACH OF THE BETA, DELTA, AND GAMMA CHAINS
Source: (synth.) TORPEDO CALIFORNICA (Pacific electric ray) / References: UniProt: P02710
Compound detailsTHE COMPLETE RECEPTOR CONSISTS OF A PENTAMER OF TWO ALPHA CHAINS, AND ONE EACH OF THE BETA, DELTA, ...THE COMPLETE RECEPTOR CONSISTS OF A PENTAMER OF TWO ALPHA CHAINS, AND ONE EACH OF THE BETA, DELTA, AND GAMMA CHAINS. THE PEPTIDE STUDIED HERE REPRESENTS THE SECOND TRANS-MEMBRANE SEGMENT OF THE ALPHA CHAIN OF ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN (RESIDUES 267 TO 285)
Sequence detailsAMINO ACIDS NUMERATION IN THE ENTRY DOES NOT INCLUDE THE SIGNAL SEQUENCE. THE C-TERMINAL RESIDUE OF ...AMINO ACIDS NUMERATION IN THE ENTRY DOES NOT INCLUDE THE SIGNAL SEQUENCE. THE C-TERMINAL RESIDUE OF THIS ENTRY, THR267, IS AMIDATED.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
131NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 2D-1H-NMR SPECTROSCOPY IN THE MEDIUM WHICH SHOULD BE ADEQUATE FOR THE M2 SEGMENT WITH ITS NON-LIPID SURROUNDING IN THE INTACT NICOTINIC ACTYLCHOLINE RECEPTOR. ...Text: THE STRUCTURE WAS DETERMINED USING 2D-1H-NMR SPECTROSCOPY IN THE MEDIUM WHICH SHOULD BE ADEQUATE FOR THE M2 SEGMENT WITH ITS NON-LIPID SURROUNDING IN THE INTACT NICOTINIC ACTYLCHOLINE RECEPTOR. THE PH GIVEN IN THE EXPERIMENTAL DETAILS IS AN APPROXIMATION ONLY FOR THE MIXTURE OF ORGANIC SOLVENTS USED.

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Sample preparation

DetailsContents: CDCL3/CD3OH=1/1 WITH 0.1 M LICLO4
Sample conditionsIonic strength: 0.1 M LICLO4 / pH: 4 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
FANTOM4R.FRACZKIEWICZ,C.MUMENTHALER,B. VON FREYBERG, T.SCHAUMANN,W.BRAUNrefinement
VARIAN VNMRVNMRstructure solution
XEASYstructure solution
DYANAstructure solution
MARDIGRASstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE NMR STUDY HAS BEEN CONDUCTED USING THE SYNTHETIC PEPTIDE WITH METHIONINE 243 REPLACED BY NORLEUCINE. SUCH AN ISOSTERIC ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE NMR STUDY HAS BEEN CONDUCTED USING THE SYNTHETIC PEPTIDE WITH METHIONINE 243 REPLACED BY NORLEUCINE. SUCH AN ISOSTERIC REPLACEMENT USUALLY DOES NOT AFFECT THE PEPTIDE CONFORMATION, WHILE SYMPLIFYING THE SYNTHESIS. TO AVOID DIFFICULTIES WHICH MAY ARISE FROM THE PRESENCE OF A NONSTANDARD AMINO ACID RESIDUE AS WELL AS FOR THE PURPOSE OF AGREEMENT BETWEEN THE NATIVE M2 FRAGMENT AND THE CONFORMERS TO BE DEPOSITED, THE NORLEUCINE RESIDUE WAS REPLACED BY METHIONINE.
NMR ensembleConformer selection criteria: LEAST RESTRAINTS VIOLATION / Conformers calculated total number: 300 / Conformers submitted total number: 20

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