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- PDB-6rc7: NMR structure of cytotoxin 3 from Naja kaouthia in solution, majo... -

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Basic information

Entry
Database: PDB / ID: 6rc7
TitleNMR structure of cytotoxin 3 from Naja kaouthia in solution, major form
ComponentsCytotoxin 3
KeywordsTOXIN / Three-finger toxin / Cobra snake venom / beta-structure / cytolytic peptide / disulfide-rich protein
Function / homology
Function and homology information


cytolysis / other organism cell membrane / : / toxin activity / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesNaja kaouthia (monocled cobra)
MethodSOLUTION NMR / simulated annealing
AuthorsDubinnyi, M.A. / Dubovskii, P.V. / Utkin, Y.N. / Arseniev, A.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: The omega-loop of cobra cytotoxins tolerates multiple amino acid substitutions.
Authors: Dubinnyi, M.A. / Dubovskii, P.V. / Starkov, V.G. / Utkin, Y.N.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxin 3


Theoretical massNumber of molelcules
Total (without water)6,7281
Polymers6,7281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4230 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Cytotoxin 3 / CX3 / Toxin CM-7


Mass: 6728.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Major form with trans configuration of ILE7-PRO8 peptide bond
Source: (natural) Naja kaouthia (monocled cobra) / Organ: Venom gland / Plasmid details: Purified from crude venom / References: UniProt: P01446

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H TOCSY
121isotropic22D DQF-COSY
131isotropic22D 1H-1H NOESY
141isotropic22D ROESY
151isotropic32D 1H-13C HSQC
161isotropic32D 1H-15N HSQC
171isotropic32D 1H-13C HSQC-TOCSY
282isotropic12D DQF-COSY
292isotropic12D 1H-1H NOESY
2102isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution13 mM No Cytotoxin 3 from Naja kaouthia, 2 mM No Cytotoxin 2 from Naja kaouthia, 90% H2O/10% D2OMixture of two cytotoxins, which could not be chromatographically separatedCT3nk_H2O90% H2O/10% D2O
solution23 mM No Cytotoxin 3 from Naja kaouthia, 2 mM No Cytotoxin 2 from Naja kaouthia, 100% D2OMixture of two cytotoxins, which could not be chromatographically separatedCT3nk_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMCytotoxin 3 from Naja kaouthiaNo1
2 mMCytotoxin 2 from Naja kaouthiaNo1
3 mMCytotoxin 3 from Naja kaouthiaNo2
2 mMCytotoxin 2 from Naja kaouthiaNo2
Sample conditions

Ionic strength: 0 mM / Ionic strength err: _ / PH err: 0.05 / Pressure: 1 bar / Pressure err: 0.01 / Temperature: 303 K / Temperature err: 1

Conditions-IDLabelpH
1CT3nk_H2O_pH4.004.00
2CT3nk_D2O_pH4.004.0 pD

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCE IIBrukerAVANCE II8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
CARA1.9.1.4Keller and Wuthrichchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichstructure calculation
TALOS1.9.1.4Cornilescu, Delaglio and Baxstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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