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- PDB-6nk9: Solution structure of AcaTx1, a potassium channel inhibitor from ... -

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Basic information

Entry
Database: PDB / ID: 6nk9
TitleSolution structure of AcaTx1, a potassium channel inhibitor from the sea anemone Antopleura cascaia
ComponentsAca Toxin 1
KeywordsTOXIN / potassium channel inhibitor / pore-blocking / neurotoxin
Biological speciesAnthopleura (sea anemone)
MethodSOLUTION NMR / molecular dynamics
AuthorsAmorim, G.C. / Madio, B. / Almeida, F.C.L.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: To Be Published
Title: Structural Features of Potassium Channel Inhibition By Acatx1, A Novel Sea Anemone Neurotoxin.
Authors: Amorim, G.C. / Almeida, F.C.L. / Madio, B.
History
DepositionJan 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aca Toxin 1


Theoretical massNumber of molelcules
Total (without water)3,3491
Polymers3,3491
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Aca Toxin 1


Mass: 3348.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anthopleura (sea anemone) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
181isotropic22D 1H-13C HSQC
191isotropic13D HNCO
131isotropic13D HN(CA)CO
141isotropic13D HN(CA)CB
271isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HBHA(CO)NH
1101isotropic13D (HB)CB(CGCD)HD
1111isotropic13D (HB)CB(CGCDCE)HE
1142isotropic23D 1H-15N NOESY
1131isotropic23D 1H-13C NOESY aliphatic
1121isotropic23D 1H-13C NOESY aromatic
1151isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1150 uM [U-99% 13C; U-99% 15N] AcaTx1, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O15N13C90% H2O/10% D2O
solution2150 uM [U-99% 15N] AcaTx1, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 uMAcaTx1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
150 uMAcaTx1[U-99% 15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMconditions_17.0 1 atm298 K
250 mMconditions_27 1 atm278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
AnalysisVranken et al., 2005data analysis
AnalysisVranken et al., 2005chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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