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- PDB-1kc4: NMR Structural Analysis of the Complex Formed Between alpha-Bunga... -

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Basic information

Entry
Database: PDB / ID: 1kc4
TitleNMR Structural Analysis of the Complex Formed Between alpha-Bungarotoxin and the Principal alpha-Neurotoxin Binding Sequence on the alpha7 Subunit of a Neuronal Nicotinic Acetylcholine Receptor
Components
  • alpha-bungarotoxin
  • neuronal acetylcholine receptor protein, alpha-7 chain
KeywordsTOXIN / alpha-bungarotoxin / nicotinic acetylcholine receptor alpha 7 subunit / alpha-neurotoxin / ligand-gated ion channels / protein-protein interactions / protein-peptide complex
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / ion channel regulator activity / chloride channel regulator activity / acetylcholine binding / synaptic transmission, cholinergic / negative regulation of tumor necrosis factor production / toxic substance binding ...acetylcholine receptor activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / ion channel regulator activity / chloride channel regulator activity / acetylcholine binding / synaptic transmission, cholinergic / negative regulation of tumor necrosis factor production / toxic substance binding / negative regulation of cytokine production involved in inflammatory response / response to nicotine / regulation of membrane potential / cognition / positive regulation of angiogenesis / intracellular calcium ion homeostasis / calcium ion transport / amyloid-beta binding / toxin activity / monoatomic ion transmembrane transport / perikaryon / chemical synaptic transmission / postsynaptic membrane / response to hypoxia / neuron projection / positive regulation of MAPK cascade / axon / positive regulation of cell population proliferation / synapse / dendrite / signal transduction / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Nicotinic acetylcholine receptor / Snake toxin-like superfamily ...Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Nicotinic acetylcholine receptor / 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
Neuronal acetylcholine receptor subunit alpha-7 / Alpha-bungarotoxin
Similarity search - Component
Biological speciesGallus gallus (chicken)
Bungarus multicinctus (many-banded krait)
MethodSOLUTION NMR / distance geometry dynamical simulated annealing
AuthorsMoise, L. / Piserchio, A. / Basus, V.J. / Hawrot, E.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: NMR structural analysis of alpha-bungarotoxin and its complex with the principal alpha-neurotoxin-binding sequence on the alpha 7 subunit of a neuronal nicotinic acetylcholine receptor.
Authors: Moise, L. / Piserchio, A. / Basus, V.J. / Hawrot, E.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Chimeric analysis of a neuronal nicotinic acetylcholine receptor reveals amino acids conferring sensitivity to alpha-bungarotoxin.
Authors: Levandoski, M.M. / Lin, Y. / Moise, L. / McLaughlin, J.T. / Cooper, E. / Hawrot, E.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Identification of sequence segments forming the alpha-bungarotoxin binding sites on two nicotinic acetylcholine receptor alpha subunits from the avian brain.
Authors: McLane, K.E. / Wu, X.D. / Schoepfer, R. / Lindstrom, J.M. / Conti-Tronconi, B.M.
#3: Journal: Biochemistry / Year: 1988
Title: Structural studies of alpha-bungarotoxin. 1. Sequence-specific 1H NMR resonance assignments.
Authors: Basus, V.J. / Billeter, M. / Love, R.A. / Stroud, R.M. / Kuntz, I.D.
History
DepositionNov 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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 / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha-bungarotoxin
B: neuronal acetylcholine receptor protein, alpha-7 chain


Theoretical massNumber of molelcules
Total (without water)10,3542
Polymers10,3542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -The submitted conformer models are the 10 with the lowest energy from a pool of over 100 accepted structures that had no restraint violations.
RepresentativeModel #1determined by nmrclust 1.2

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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 / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60615
#2: Protein/peptide neuronal acetylcholine receptor protein, alpha-7 chain


Mass: 2348.629 Da / Num. of mol.: 1 / Fragment: alpha-neurotoxin binding site
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET31b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS / References: UniProt: P22770

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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
1413D 15N-separated TOCSY
1512D 1H-15N HSQC
161HNHA
NMR detailsText: THE WELL-DEFINED REGIONS IN THE COMPLEX, EXHIBITING EXTENSIVE LONG RANGE NOES, ARE: BGTX: 1-16, 22-28, 39-48, AND 54-68 ALPHA 7 19MER: 185-194

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6 mM alpha-bungarotoxin/[U-15N]-alpha 7 19mer complex 30 mM sodium phosphate, pH 5.5 50 micromolar sodium azide 50 micromolar TMSP95% H2O/5% D2O
21.6 mM alpha-bungarotoxin/[U-15N]-alpha 7 19mer complex 30 mM sodium phosphate, pH 5.5 50 micromolar sodium azide 50 micromolar TMSP99.9% D2O
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 308 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 AVANCEBrukerAVANCE4002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1collection
NMRPipe1.8Delaglio, F., et al.processing
Sparky3.87Goddard, T.D. and Kneller, D.G.data analysis
CNS1Brunger, A.T., et al.refinement
RefinementMethod: distance geometry dynamical simulated annealing / Software ordinal: 1
Details: RMS DEVIATIONS FROM IDEAL VALUES: BOND LENGTH(A) 0.0039, ANGLES(DEG) 0.61, IMPROPERS(DEG) 0.53
NMR representativeSelection criteria: determined by nmrclust 1.2
NMR ensembleConformer selection criteria: The submitted conformer models are the 10 with the lowest energy from a pool of over 100 accepted structures that had no restraint violations.
Conformers submitted total number: 10

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