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- PDB-5nq4: Cytotoxin-1 in DPC-micelle -

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Basic information

Entry
Database: PDB / ID: 5nq4
TitleCytotoxin-1 in DPC-micelle
ComponentsCytotoxin 1
KeywordsTOXIN / cytolytic peptide / cobra venom / cytotoxyc activity / three-finger protein
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
Biological speciesNaja oxiana (Central Asian cobra)
MethodSOLUTION NMR / simulated annealing
AuthorsDubovskii, P.V. / Dubinnyi, M.A. / Volynsky, P.E. / Pustovalova, Y.E. / Konshina, A.G. / Utkin, Y.N. / Efremov, R.G. / Arseniev, A.S.
Citation
Journal: J. Biomol. Struct. Dyn. / Year: 2018
Title: Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin.
Authors: Dubovskii, P.V. / Dubinnyi, M.A. / Volynsky, P.E. / Pustovalova, Y.E. / Konshina, A.G. / Utkin, Y.N. / Arseniev, A.S. / Efremov, R.G.
#1: Journal: Biochem. J. / Year: 2005
Title: Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins.
Authors: Dubovskii, P.V. / Lesovoy, D.M. / Dubinnyi, M.A. / Konshina, A.G. / Utkin, Y.N. / Efremov, R.G. / Arseniev, A.S.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 2.0Feb 21, 2018Group: Atomic model / Category: atom_site
Revision 2.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 2.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.3Nov 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxin 1


Theoretical massNumber of molelcules
Total (without water)6,8311
Polymers6,8311
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: the toxin molecule is a monomer under conditions chosen, approximately 60 molecules of detergent
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4280 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Cytotoxin 1 / Cytotoxin I / CTI


Mass: 6831.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja oxiana (Central Asian cobra) / Production host: Naja oxiana (Central Asian cobra) / References: UniProt: P01451
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D DQF-COSY
141isotropic2diffusion
252isotropic12D 1H-1H NOESY
262isotropic12D 1H-1H TOCSY
272isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution13.0 mM no cytotoxin-1, 180.0 mM fully deuterated dodecylphosphocholine, 50 mM no potassium chloride, 50 M no H2O, 5.5 M 99.9%-deuterated D2O, 0.01 uM no HCl, 90% H2O/10% D2Ocytoxin-1 in deuterated dodecylphosphocholine (DPC)condition_190% H2O/10% D2O
solution23.0 mM no cytotoxin-1, 180.0 mM fully deuterated dodecylphosphocholine, 50 mM no potassium chloride, 55 M 100%-deuterated D2O, 0.01 uM no HCl, 100% D2Osame as at condition_1, but in D2Ocondition_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.0 mMcytotoxin-1no1
180.0 mMdodecylphosphocholinefully deuterated1
50 mMpotassium chlorideno1
50 MH2Ono1
5.5 MD2O99.9%-deuterated1
0.01 uMHClno1
3.0 mMcytotoxin-1no2
180.0 mMdodecylphosphocholinefully deuterated2
50 mMpotassium chlorideno2
55 MD2O100%-deuterated2
0.01 uMHClno2
Sample conditions

Ionic strength: 50 mM / Ionic strength err: 0.2 / PH err: 0.1 / Pressure: 1 bar / Pressure err: 0.01 / Temperature: 323 K / Temperature err: 0.1

Conditions-IDLabelpH
1condition_16
2condition_26.0 pD

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian UNITYVarianUNITY6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Biospincollection
NMRPipe2001.085.20.47Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA1.0.6Guntert, Mumenthaler and Wuthrichstructure calculation
XEASY1.2.11Bartels et al.chemical shift assignment
XEASYBartels et al.peak picking
RefinementMethod: simulated annealing / Software ordinal: 2
Details: the structures are based on 517 NOE constraints, 160 hudrogen bond and 24 disulfide bond constraints, and 236 constraints for 193 angles
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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