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- PDB-1lxg: Solution structure of alpha-cobratoxin complexed with a cognate p... -

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Basic information

Entry
Database: PDB / ID: 1lxg
TitleSolution structure of alpha-cobratoxin complexed with a cognate peptide (structure ensemble)
Components
  • Acetylcholine receptor protein, alpha chain
  • Long neurotoxin 1
KeywordsTOXIN / alpha-cobratoxin / nicotinic acetylcholine receptor / protein-protein 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, 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 ...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
Alpha-cobratoxin / Acetylcholine receptor subunit alpha
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
Naja kaouthia (monocled cobra)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsZeng, H. / Hawrot, E.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: NMR-based Binding Screen and Structural Analysis of the Complex Formed between alpha-Cobratoxin and an 18-mer Cognate Peptide Derived from the alpha1 Subunit of the Nicotinic Acetylcholine ...Title: NMR-based Binding Screen and Structural Analysis of the Complex Formed between alpha-Cobratoxin and an 18-mer Cognate Peptide Derived from the alpha1 Subunit of the Nicotinic Acetylcholine Receptor from Torpedo californica
Authors: Zeng, H. / Hawrot, E.
History
DepositionJun 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / 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: Long neurotoxin 1
B: Acetylcholine receptor protein, alpha chain


Theoretical massNumber of molelcules
Total (without water)10,2672
Polymers10,2672
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)10 / 100structures with the lowest energy
RepresentativeModel #5lowest energy

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Components

#1: Protein Long neurotoxin 1 / Neurotoxin 3 / Alpha-cobratoxin


Mass: 7842.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: P01391
#2: Protein/peptide Acetylcholine receptor protein, alpha chain


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
111HSQC
1213D TOCSY-HSQC
1313D NOESY-HSQC
141HNHA
1512D TOCSY
1612D NOESY

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Sample preparation

DetailsContents: 1.6 mM alpha-cobratoxin/alpha18-mer complex, alpha18-mer is U-15N, 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 / 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 spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
NMRPipe1.8Delaglio, F. et al.processing
Sparky3.95Goddard, T.D. et al.data analysis
CNS1.1Brunger, A.T. et al.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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