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- PDB-1idh: THE NMR SOLUTION STRUCTURE OF THE COMPLEX FORMED BETWEEN ALPHA-BU... -

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Basic information

Entry
Database: PDB / ID: 1idh
TitleTHE NMR SOLUTION STRUCTURE OF THE COMPLEX FORMED BETWEEN ALPHA-BUNGAROTOXIN AND AN 18MER COGNATE PEPTIDE
Components
  • ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN
  • ALPHA-BUNGAROTOXIN
KeywordsTOXIN / ALPHA-BUNGAROTOXIN / NICOTINIC ACETYLCHOLINE RECEPTOR / ALPHA 1 SUBUNIT / PROTEIN-PROTEIN INTERACTION / CATION-PI INTERACTION
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / ion channel regulator activity / transmembrane signaling receptor activity / toxin activity / postsynaptic membrane / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Nicotinic acetylcholine receptor / CD59 / CD59 / Snake toxin-like superfamily / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. ...Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Nicotinic acetylcholine receptor / CD59 / CD59 / Snake toxin-like superfamily / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Alpha-bungarotoxin
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
Bungarus multicinctus (many-banded krait)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsZeng, H. / Moise, L. / Grant, M.A. / Hawrot, E.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The solution structure of the complex formed between alpha-bungarotoxin and an 18-mer cognate peptide derived from the alpha 1 subunit of the nicotinic acetylcholine receptor from Torpedo californica.
Authors: Zeng, H. / Moise, L. / Grant, M.A. / Hawrot, E.
History
DepositionApr 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-BUNGAROTOXIN
B: ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)10,4302
Polymers10,4302
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)20 / 300The submitted conformer models are the 20 structures with the lowest energy from 120 acceptable structures which were from 300 total calculated structures and had no restraint violations. The best representative conformer is the lowest potential energy structure of the ensemble.
RepresentativeModel #8it is the lowest potential energy structure of the ensemble

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Components

#1: Protein ALPHA-BUNGAROTOXIN / LONG NEUROTOXIN 1


Mass: 8005.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURCHASED FROM SIGMA / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60615
#2: Protein/peptide ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN / / NACHR-ALPHA1-SUBUNIT


Mass: 2424.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Torpedo californica (Pacific electric ray)
Plasmid: PET-31B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02710

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated TOCSY
1213D HNHA
1313D 15N-separated NOESY
1412D TOCSY
1512D NOESY
1612D 1H-15N HSQC
NMR detailsText: The authors recommend using the Graphics program, MOLMOL, to view this ensemble of 20 structures.

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Sample preparation

DetailsContents: 2.1 mM alpha-Bungarotoxin/alpha18mer complex, alpha18mer is 15N labeled, 50 mM perdeuterated potassium acetate buffer (pH 4.0) with 5% D2O and 0.05% sodium azide
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 4.0 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
NMRPipe1.8Delaglio, F. et al.processing
Sparky3.95Goddard, T.D. and Kneller, D.G.data analysis
CNSsolve1Brunger, A.T. et al.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: it is the lowest potential energy structure of the ensemble
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest energy from 120 acceptable structures which were from 300 total calculated structures and had no ...Conformer selection criteria: The submitted conformer models are the 20 structures with the lowest energy from 120 acceptable structures which were from 300 total calculated structures and had no restraint violations. The best representative conformer is the lowest potential energy structure of the ensemble.
Conformers calculated total number: 300 / Conformers submitted total number: 20

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