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- PDB-7tvr: Structure of the ribbon isoform of the novel conotoxin PnID deriv... -

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Basic information

Entry
Database: PDB / ID: 7tvr
TitleStructure of the ribbon isoform of the novel conotoxin PnID derived from Conus pennaceus
ComponentsChi-conotoxin-like PnMRCL-013
KeywordsTOXIN / Venom peptide / conotoxin
Function / homologyT-superfamily conotoxin / chi-Conotoxin or t superfamily / toxin activity / extracellular region / Chi-conotoxin-like PnMRCL-013
Function and homology information
Biological speciesConus pennaceus (invertebrata)
MethodSOLUTION NMR / molecular dynamics
AuthorsLoening, N.M. / Espiritu, M.J.
Funding support United States, 6items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1917696 United States
Other privateM. J. Murdock Charitable Trust Grant 201811283
United States Department of Agriculture (USDA)HATCH (HAW00595-R) United States
United States Department of Agriculture (USDA)NIFA (#2011-37610-31182) United States
Other governmentFulbright - Philippine Agriculture Scholarship Program for Advanced Research
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA00522 United States
CitationJournal: Mar Drugs / Year: 2023
Title: Characterization of the Native Disulfide Isomers of the Novel chi-Conotoxin PnID: Implications for Further Increasing Conotoxin Diversity.
Authors: Espiritu, M.J. / Taylor, J.K. / Sugai, C.K. / Thapa, P. / Loening, N.M. / Gusman, E. / Baoanan, Z.G. / Baumann, M.H. / Bingham, J.P.
History
DepositionFeb 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _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: Chi-conotoxin-like PnMRCL-013


Theoretical massNumber of molelcules
Total (without water)1,3221
Polymers1,3221
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Chi-conotoxin-like PnMRCL-013


Mass: 1321.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus pennaceus (invertebrata) / References: UniProt: Q9BPE9
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM PnID (ribbon form), 0.2 mM DSS, 95% H2O/5% D2O
Details: pH adjusted to 4.0 with HCl. / Label: PnID_b / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPnID (ribbon form)natural abundance1
0.2 mMDSSnatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 4.0 / PH err: 0.1 / Pressure: 1 atm / Temperature: 278 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz / Details: room temperature TXI probe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.5.2CCPNchemical shift assignment
TopSpin4.1.3Bruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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