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- PDB-1abt: NMR SOLUTION STRUCTURE OF AN ALPHA-BUNGAROTOXIN(SLASH)NICOTINIC R... -

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Basic information

Entry
Database: PDB / ID: 1abt
TitleNMR SOLUTION STRUCTURE OF AN ALPHA-BUNGAROTOXIN(SLASH)NICOTINIC RECEPTOR PEPTIDE COMPLEX
Components
  • ALPHA-BUNGAROTOXIN
  • NICOTINIC RECEPTOR PEPTIDE
KeywordsTOXIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / acetylcholine-gated monoatomic cation-selective channel activity / transmembrane signaling receptor activity / postsynaptic membrane / toxin activity / neuron projection / 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
MethodSOLUTION NMR
AuthorsBasus, V.J. / Song, G. / Hawrot, E.
Citation
Journal: Biochemistry / Year: 1993
Title: NMR solution structure of an alpha-bungarotoxin/nicotinic receptor peptide complex.
Authors: Basus, V.J. / Song, G. / Hawrot, E.
#1: Journal: Proc.R.Soc.London,Ser.B / Year: 1990
Title: The Role of Tyrosine at the Ligand-Binding Site of the Nicotinic Acetylcholine Receptor
Authors: Pearce, S.F.A. / Preston-Hurlburt, P. / Hawrot, E.
#2: 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 17, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-BUNGAROTOXIN
B: NICOTINIC RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)9,5232
Polymers9,5232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: TYR A 24 - ARG A 25 MODEL 1 OMEGA =228.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CYS A 29 - ASP A 30 MODEL 1 OMEGA = 17.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: GLU A 41 - LEU A 42 MODEL 2 OMEGA =134.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: LYS A 38 - VAL A 39 MODEL 3 OMEGA =145.32 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: TYR A 24 - ARG A 25 MODEL 4 OMEGA = 9.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: VAL A 39 - VAL A 40 MODEL 4 OMEGA =210.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: VAL A 40 - GLU A 41 MODEL 4 OMEGA =128.73 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / -
Representative

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Components

#1: Protein ALPHA-BUNGAROTOXIN


Mass: 8005.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P60615
#2: Protein/peptide NICOTINIC RECEPTOR PEPTIDE


Mass: 1517.726 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P02710

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameDeveloperClassification
VEMBEDKUNTZrefinement
GROMOS-87VAN GUNSTERENrefinement
RefinementSoftware ordinal: 1
Details: NOE DATA CAME FROM SPECTRA COLLECTED AT 35 DEGREES AND AT 25 DEGREES CELSIUS, PH 5.8. A LIST OF ALL NMR CONSTRAINTS WAS DEPOSITED IN THE PROTEIN DATA BANK TOGETHER WITH THE STRUCTURE LIST. ...Details: NOE DATA CAME FROM SPECTRA COLLECTED AT 35 DEGREES AND AT 25 DEGREES CELSIUS, PH 5.8. A LIST OF ALL NMR CONSTRAINTS WAS DEPOSITED IN THE PROTEIN DATA BANK TOGETHER WITH THE STRUCTURE LIST. THESE CONSTRAINTS CONSISTED OF 365 INTRAMOLECULAR CONSTRAINTS (146 LONG-RANGE, 155 SEQUENTIAL AND 64 DIHEDRAL ANGLES), AND 24 INTERMOLECULAR CONSTRAINTS BETWEEN THE 74 RESIDUES OF BGTX AND THE FIRST 6 RESIDUES OF THE 12 RESIDUE PEPTIDE FRAGMENT OF NACHR USED IN THIS STUDY (LISTED HERE AS RESIDUES 75 B - 80 B). THE COORDINATES THAT FOLLOW ARE IN FOUR SEPARATE MODELS. THE 12 RESIDUE PEPTIDE FRAGMENT OF NACHR HAS BEEN MODELED FOR ONLY THE FIRST SIX RESIDUES AND HAS BEEN NUMBERED AS A CONTINUATION OF THE NUMBERS FOR THE BGTX PORTION OF THE COMPLEX AND GIVEN THE CHAIN IDENTIFIER 'B', AFTER THE TER ENTRY SEPARATING THE COORDINATES OF THE TWO COMPONENTS OF THE COMPLEX. THE AVERAGE RMS DEVIATION OF THE BACKBONE ATOMS, WHEN MATCHED IN A PAIRWISE MANNER, IS 2.6 ANGSTROMS, WITH THE POORLY DEFINED REGIONS OF RESIDUES 30 A - 38 A, AND 69 A - 74 A OF BGTX EXCLUDED. RESTRAINT VIOLATIONS: VIOLATIONS WERE CATEGORIZED ACCORDING TO SIZE. THE TOTAL NUMBER OF VIOLATIONS IN EACH CATEGORY WAS ADDED, AND THAT NUMBER DIVIDED BY 4 TO DETERMINE THE AVERAGE NUMBER OF VIOLATIONS PER STRUCTURE FOR EACH CATEGORY. VIOLATION RANGE AVERAGE NUMBER OF VIOLATIONS (ANGSTROMS) VIOLATION >0.7 5.0 0.7>=VIOLATION >0.6 6.0 0.6>=VIOLATION >0.5 5.75 0.5>=VIOLATION >0.4 9.5 0.4>=VIOLATION >0.3 17.0 0.3>=VIOLATION >0.2 16.5 0.2>=VIOLATION >0.1 18.0. TO SIMPLIFY THE CALCULATIONS, ONLY THE FIRST SIX AMINO ACIDS (185 - 190) OF THE DODECAPEPTIDE WERE INCORPORATED INTO THE STRUCTURE OF THE COMPLEX. THIS WAS APPROPRIATE AS NO INTERMOLECULAR NOE'S AND NO LONG-RANGE INTRAMOLECULAR NOE'S WERE ASSIGNED INVOLVING PEPTIDE RESIDUES 191 - 196. THE COORDINATES ARE PRESENTED IN FOUR SEPARATE MODELS, WITH TER STATEMENTS TO SEPARATE THE BGTX PART OF THE COMPLEX FROM THE NACHR PORTION OF THE COMPLEX. ALL STRUCTURES WERE MATCHED IN CARTESIAN SPACE SUCH THAT THE RMSD BETWEEN THEM WAS MINIMIZED, WITH THE EXCLUSION OF RESIDUES 30 A - 38 A, AND 69 A - 74 A OF BGTX.
NMR ensembleConformers submitted total number: 4

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