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- PDB-7bwi: Solution structure of recombinant APETx1 -

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Basic information

Entry
Database: PDB / ID: 7bwi
TitleSolution structure of recombinant APETx1
ComponentsKappa-actitoxin-Ael2a
KeywordsTOXIN
Function / homology
Function and homology information


nematocyst / ion channel inhibitor activity / potassium channel regulator activity / sodium channel regulator activity / toxin activity / defense response to bacterium / extracellular region
Similarity search - Function
BDS potassium channel toxin / Potassium-channel blocking toxin / Myotoxin/Anemone neurotoxin domain superfamily
Similarity search - Domain/homology
Kappa-actitoxin-Ael2a
Similarity search - Component
Biological speciesAnthopleura elegantissima (clonal anemone)
MethodSOLUTION NMR / molecular dynamics
AuthorsMatsumura, K. / Kobayashi, N. / Kurita, J. / Nishimura, Y. / Yokogawa, M. / Imai, S. / Shimada, I. / Osawa, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H03978 Japan
CitationJournal: Bmc Mol Cell Biol / Year: 2021
Title: Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization.
Authors: Matsumura, K. / Shimomura, T. / Kubo, Y. / Oka, T. / Kobayashi, N. / Imai, S. / Yanase, N. / Akimoto, M. / Fukuda, M. / Yokogawa, M. / Ikeda, K. / Kurita, J.I. / Nishimura, Y. / Shimada, I. / Osawa, M.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-actitoxin-Ael2a


Theoretical massNumber of molelcules
Total (without water)4,5611
Polymers4,5611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Kappa-actitoxin-Ael2a / Kappa-AITX-Ael2a / Toxin APETx1


Mass: 4561.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anthopleura elegantissima (clonal anemone)
Production host: Escherichia coli (E. coli) / References: UniProt: P61541

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic23D HN(CA)CB
151isotropic23D CBCA(CO)NH
161isotropic23D HNCO
181isotropic23D (H)CCH-TOCSY
171isotropic23D (H)CCH-COSY
1121isotropic23D 1H-15N TOCSY
1151isotropic23D 1H-15N NOESY
1141isotropic23D 1H-13C NOESY aliphatic
1131isotropic23D 1H-13C NOESY aromatic
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.691 mM [U-100% 13C; U-100% 15N] APETx1, 20 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O
Label: APETx1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.691 mMAPETx1[U-100% 13C; U-100% 15N]1
20 mMpotassium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 120 mM / Label: APETx1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD7001
Bruker Avance 600BrukerAvance 6006002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
MAGRO2.01.28Kobayashi, N.peak picking
NMRViewJohnson, One Moon Scientificdata analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
MAGRO2.01.28Kobayashi, N.data analysis
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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