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- PDB-5lue: Minor form of the recombinant cytotoxin-1 from N. oxiana -

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Basic information

Entry
Database: PDB / ID: 5lue
TitleMinor form of the recombinant cytotoxin-1 from N. oxiana
ComponentsVC-1=CYTOTOXIN
KeywordsTOXIN / cytolytic peptide / all-beta sheet protein / cobra venom / Structure from MOLMOL
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Cytotoxin 1 / VC-1=CYTOTOXIN
Similarity search - Component
Biological speciesNaja oxiana (Central Asian cobra)
MethodSOLUTION NMR / restrained Rosetta minimization
AuthorsDubovskii, P.V. / Dubinnyi, M.A. / Shulepko, M.A. / Lyukmanova, E.N. / Dolgikh, D.A. / Kirpichnikov, M.P. / Efremov, R.G.
Funding support Russian Federation, 6items
OrganizationGrant numberCountry
RFBR13-04-02128 Russian Federation
RFBR14-14-00255 Russian Federation
RFBR16-04-01479 Russian Federation
RFBR16-04-00578 Russian Federation
President of Russian FederationSP-2663.2015.4 Russian Federation
Russian Academy of SciencesProgram "Molecular and Cellular Biology" Russian Federation
Citation
Journal: Biochemistry / Year: 2017
Title: Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They?
Authors: Dubovskii, P.V. / Dubinnyi, M.A. / Konshina, A.G. / Kazakova, E.D. / Sorokoumova, G.M. / Ilyasova, T.M. / Shulepko, M.A. / Chertkova, R.V. / Lyukmanova, E.N. / Dolgikh, D.A. / Arseniev, A.S. / Efremov, R.G.
#1: Journal: To Be Published
Title: Towards universal approach for bacterial production of three-finger Ly6/uPAR proteins: case study of Cytotoxin I from cobra N. oxiana
Authors: Shulepko, M.A. / Lyukmanova, E.N. / Shenkarev, Z.O. / Dubovskii, P.V. / Astapova, M.V. / Feofanov, A.V. / Arseniev, A.S. / Utkin, Y.N. / Kirpichnikov, M.P. / Dolgikh, D.A.
History
DepositionSep 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VC-1=CYTOTOXIN


Theoretical massNumber of molelcules
Total (without water)6,9631
Polymers6,9631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4290 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #17quality score

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Components

#1: Protein VC-1=CYTOTOXIN / cytotoxin-1


Mass: 6962.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The toxin gene encoding 60 amino acid residues with additional ATG codon at the 5(prime)-end was constructed from six overlapping synthetic oligonucleotides using PCR
Source: (gene. exp.) Naja oxiana (Central Asian cobra) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9PS33, UniProt: P01451*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D HN(COCA)CB
151isotropic13D (H)CCH-TOCSY
161isotropic12D 1H-15N HSQC
171isotropic12D 1H-13C HSQC aliphatic
181isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY aliphatic
1101isotropic21D WATERGATE

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] recombinant cytotoxin-1, 95 v/v non-labeled H2O, 5 v/v 99.9%-2H D2O, 3 uM non-labeled NaOH, 1 uM non-labeled HCl, 95% H2O/5% D2O
Details: uniformly labeled 13C-15N recombinant toxin was dissolved in H2O/D2O(95:5 v/v) mixture and pH was adjusted with small additions of concentrated NaOH, HCl solutions
Label: 13C-15N sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMrecombinant cytotoxin-1[U-99% 13C; U-99% 15N]1
95 v/vH2Onon-labeled1
5 v/vD2O99.9%-2H1
3 uMNaOHnon-labeled1
1 uMHClnon-labeled1
Sample conditionsDetails: identical to those used at the investigation of the native toxin (deposited under code of 1RL5)
Ionic strength: 0 Not defined / Ionic strength err: 0.1 / Label: conditions_1 / pH: 6.5 / PH err: 0.1 / Pressure: 101325 Pa / Pressure err: 100 / Temperature: 303 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.0.aBruker Biospincollection
CARA1.8.4Keller and Wuthrichchemical shift assignment
CYANA1.0.6Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8.4Keller and Wuthrichchemical shift assignment
Rosetta3.3David Bakerrefinement
RefinementMethod: restrained Rosetta minimization / Software ordinal: 4
Details: as in: J Am Chem Soc. 2014 Feb 5;136(5):1893-906. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. Mao B, Tejero R, Baker D, Montelione GT.
NMR representativeSelection criteria: quality score
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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