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- PDB-8b1l: NMR structure of the antimicrobial peptide Of-Pis1 in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 8b1l
TitleNMR structure of the antimicrobial peptide Of-Pis1 in DPC micelles
ComponentsPiscidin
KeywordsANTIMICROBIAL PROTEIN / Piscidin / histidine-rich peptide / membrane interaction
Function / homologyPleurocidin / Pleurocidin family / defense response to bacterium / Piscidin
Function and homology information
Biological speciesOplegnathus fasciatus (barred knifejaw)
MethodSOLUTION NMR / simulated annealing
AuthorsAlaimo, N. / Bischetti, M. / Gallo, M. / Cicero, D.O.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other government Italy
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2022
Title: Structural insights on the selective interaction of the histidine-rich piscidin antimicrobial peptide Of-Pis1 with membranes.
Authors: Bischetti, M. / Alaimo, N. / Nardelli, F. / Punzi, P. / Amariei, C. / Ingenito, R. / Musco, G. / Gallo, M. / Cicero, D.O.
History
DepositionSep 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Piscidin


Theoretical massNumber of molelcules
Total (without water)2,5831
Polymers2,5831
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Piscidin / Piscidin-1


Mass: 2583.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oplegnathus fasciatus (barred knifejaw) / References: UniProt: M5AE98

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC aliphatic
121isotropic12D 1H-13C HSQC aromatic
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: micelle
Contents: 3 mM Of-Pis1, 60 mM [U-2H] DPC, 20 mM sodium phosphate, 90% H2O/10% D2O
Label: DPC_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMOf-Pis1natural abundance1
60 mMDPC[U-2H]1
20 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 40 mM / Label: cond_1 / pH: 5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
Details: the structures are based on a total of 453 NOE-derived distances constraints and 17 dihedral angles restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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