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- PDB-8s9y: Taipan Natriuretic Peptide C -TNPc -

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Basic information

Entry
Database: PDB / ID: 8s9y
TitleTaipan Natriuretic Peptide C -TNPc
ComponentsPeptide TNP-c
KeywordsTOXIN / defined ring region
Function / homology
Function and homology information


hormone activity / regulation of blood pressure / vasodilation / toxin activity / extracellular region
Similarity search - Function
Natriuretic peptide, brain type / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide
Similarity search - Domain/homology
Biological speciesOxyuranus microlepidotus (cobra)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsTorres, A.M. / Alewood, P.F.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Molecules / Year: 2023
Title: Taipan Natriuretic Peptides Are Potent and Selective Agonists for the Natriuretic Peptide Receptor A.
Authors: Vink, S. / Akondi, K.B. / Jin, J. / Poth, K. / Torres, A.M. / Kuchel, P.W. / Burke, S.L. / Head, G.A. / Alewood, P.F.
History
DepositionMar 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide TNP-c


Theoretical massNumber of molelcules
Total (without water)4,1201
Polymers4,1201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptide TNP-c / Taipan natriuretic peptide / Venom natriuretic peptide OxsSNPc


Mass: 4119.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oxyuranus microlepidotus (cobra) / References: UniProt: P83230

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Experimental details

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Experiment

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

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Sample preparation

DetailsType: solution
Contents: 1 mM Taipan Natriuetic Peptide C -TNPc, 90% H2O/10% D2O
Details: dissolved in 600ul 90%H20:10%D2O / Label: TNPc / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Taipan Natriuetic Peptide C -TNPc / Isotopic labeling: natural abundance
Sample conditionsIonic strength: not known Not defined / Label: standard / pH: 4.4 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
DYANAGuntert, Braun and Wuthrichstructure calculation
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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