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- PDB-2p4l: Structure and sodium channel activity of an excitatory I1-superfa... -

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Basic information

Entry
Database: PDB / ID: 2p4l
TitleStructure and sodium channel activity of an excitatory I1-superfamily conotoxin
ComponentsI-superfamily conotoxin r11a
KeywordsTOXIN / IAA / iodoacetic acid / INa / sodium current / NEM / N-ethylmaleimide / NMR / nuclear magnetic resonance / NOE / nuclear Overhauser effect / TFA / trifluoroacetic acid / VGSC / voltage-gated sodium channel.
Function / homology
Function and homology information


sodium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Omega-AgatoxinV - #80 / Conotoxin I-superfamily / Conotoxin I-superfamily / Conotoxin-I, conserved site / I-superfamily conotoxin signature. / Omega-AgatoxinV / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesConus radiatus (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsBuczek, O. / Wei, D.X. / Babon, J.J. / Yang, X.D. / Fiedler, B. / Yoshikami, D. / Olivera, B.M. / Bulaj, G. / Norton, R.S.
CitationJournal: Biochemistry / Year: 2007
Title: Structure and Sodium Channel Activity of an Excitatory I(1)-Superfamily Conotoxin
Authors: Buczek, O. / Wei, D. / Babon, J.J. / Yang, X. / Fiedler, B. / Chen, P. / Yoshikami, D. / Olivera, B.M. / Bulaj, G. / Norton, R.S.
History
DepositionMar 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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_conn
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_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: I-superfamily conotoxin r11a


Theoretical massNumber of molelcules
Total (without water)4,9881
Polymers4,9881
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide I-superfamily conotoxin r11a / R11.6 / Conotoxin iota-RXIA


Mass: 4987.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus radiatus (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z094

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.1mM [L-Phe44] iota-RXIA-, 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionspH: 5.9 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORXplor-nih 2.9.3Schwietersrefinement
DYANACyana 1.0.6Hermannstructure solution
XEASYXeasy 1.3.13Bartelsdata analysis
Bruker BiospinXwinnmr 3.5Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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