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- PDB-5mou: NMR spatial structure of scorpion alpha-like toxin BeM9 -

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Basic information

Entry
Database: PDB / ID: 5mou
TitleNMR spatial structure of scorpion alpha-like toxin BeM9
ComponentsAlpha-mammal toxin BeM9
KeywordsPROTEIN / PROTEIN NEUROTOXIN
Function / homology
Function and homology information


sodium channel inhibitor activity / : / defense response / toxin activity / extracellular region
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-like toxin BeM9
Similarity search - Component
Biological speciesMesobuthus eupeus (lesser Asian scorpion)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMineev, K.S. / Kuldushev, N.A. / Berkut, A.A. / Grishin, E.V. / Vassilevski, A.A. / Arseniev, A.S.
CitationJournal: Proteins / Year: 2018
Title: Refined structure of BeM9 reveals arginine hand, an overlooked structural motif in scorpion toxins affecting sodium channels.
Authors: Kuldyushev, N.A. / Mineev, K.S. / Berkut, A.A. / Peigneur, S. / Arseniev, A.S. / Tytgat, J. / Grishin, E.V. / Vassilevski, A.A.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 20, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.5Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-mammal toxin BeM9


Theoretical massNumber of molelcules
Total (without water)7,3511
Polymers7,3511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4250 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Alpha-mammal toxin BeM9 / Neurotoxin M9


Mass: 7351.345 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus eupeus (lesser Asian scorpion)
Production host: Escherichia coli (E. coli) / References: UniProt: P09981

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D DQF-COSY
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-15N TOCSY
191isotropic12D 1H-15N HSQC
181isotropic12D 1H-13C HSQC aliphatic
171isotropic13D HNHA
161isotropic13D HNHB

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 15N] Alpha-mammal toxin BeM9, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Alpha-mammal toxin BeM9 / Isotopic labeling: [U-99% 15N]
Sample conditionsIonic strength: 10 mM / Label: sc_1 / pH: 3.5 / Pressure: AMBIENT Pa / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.4Keller and Wuthrichchemical shift calculation
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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