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- PDB-6pf0: SOLID-STATE NMR STRUCTURE OF PISCIDIN 1 IN ALIGNED 4:1 PHOSPHATID... -

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Basic information

Entry
Database: PDB / ID: 6pf0
TitleSOLID-STATE NMR STRUCTURE OF PISCIDIN 1 IN ALIGNED 4:1 PHOSPHATIDYLCHOLINE/CHOLESTEROL LIPID BILAYERS
ComponentsMoronecidin
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PEPTIDE / ANTICANCER PEPTIDE / ANTI HIV-1 / CATIONIC / AMPHIPATHIC / HISTIDINE RICH / HELICAL / LIPID BILAYERS / BACTERIAL CELL MEMBRANE MIMIC
Function / homologyPleurocidin / Pleurocidin family / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Moronecidin
Function and homology information
Biological speciesMorone saxatilis (striped sea-bass)
MethodSOLID-STATE NMR / simulated annealing
AuthorsGreenwood, A.I. / Cairns, L.S. / Fu, R. / Cotten, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1716608 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The host-defense peptide piscidin P1 reorganizes lipid domains in membranes and decreases activation energies in mechanosensitive ion channels.
Authors: Comert, F. / Greenwood, A. / Maramba, J. / Acevedo, R. / Lucas, L. / Kulasinghe, T. / Cairns, L.S. / Wen, Y. / Fu, R. / Hammer, J. / Blazyk, J. / Sukharev, S. / Cotten, M.L. / Mihailescu, M.
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Moronecidin


Theoretical massNumber of molelcules
Total (without water)2,5771
Polymers2,5771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint0 kcal/mol
Surface area2420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Moronecidin / Piscidin-1


Mass: 2577.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT / Source: (synth.) Morone saxatilis (striped sea-bass) / References: UniProt: Q8UUG0

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic115N 1H solid-state de-HETCOR
162anisotropic115N 1H solid-state de-HETCOR
123anisotropic115N 1H solid-state de-HETCOR
134anisotropic215N 1H solid-state de-HETCOR
145anisotropic315N 1H solid-state de-HETCOR
156anisotropic115N 1H solid-state de-HETCOR
177anisotropic115N 1H solid-state de-HETCOR
188anisotropic115N 1H solid-state de-HETCOR
199anisotropic215N 1H solid-state de-HETCOR
11010anisotropic315N 1H solid-state de-HETCOR
11111anisotropic315N 1H solid-state de-HETCOR
11212anisotropic315N 1H solid-state de-HETCOR
11313anisotropic315N 1H solid-state de-HETCOR

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
oriented membrane film110 mM [15N]-F2I5G8 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4F2-I5-G8-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film210 mM [15N]-V10G13I16 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4V10-G13-I16-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film310 mM [15N]-L19V20 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4L19-V20-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film410 mM [15N]-I9T15 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4I9-T15-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film510 mM [15N]-F6V12 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4F6-V12-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film610 mM [15N]-R18 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4R18-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film710 mM [15N]-H4 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4H4-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film810 mM [15N]-K14 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4K14-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film910 mM [15N]-R7 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4R7-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1010 mM [15N]-H11 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4H11-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1110 mM [15N]-H17 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4H17-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1210 mM [15N]-T21G22 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4T21-G22-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1310 mM [15N]-H3 Moronecidin, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4H3-15N_P1H2O 100%; phosphate buffer 40 mM pH 7.4
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMMoronecidin[15N]-F2I5G81
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance1
80 mMCholesterolnatural abundance1
10 mMMoronecidin[15N]-V10G13I162
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance2
80 mMCholesterolnatural abundance2
10 mMMoronecidin[15N]-L19V203
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance3
80 mMCholesterolnatural abundance3
10 mMMoronecidin[15N]-I9T154
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance4
80 mMCholesterolnatural abundance4
10 mMMoronecidin[15N]-F6V125
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance5
80 mMCholesterolnatural abundance5
10 mMMoronecidin[15N]-R186
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance6
80 mMCholesterolnatural abundance6
10 mMMoronecidin[15N]-H47
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance7
80 mMCholesterolnatural abundance7
10 mMMoronecidin[15N]-K148
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance8
80 mMCholesterolnatural abundance8
10 mMMoronecidin[15N]-R79
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance9
80 mMCholesterolnatural abundance9
10 mMMoronecidin[15N]-H1110
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance10
80 mMCholesterolnatural abundance10
10 mMMoronecidin[15N]-H1711
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance11
80 mMCholesterolnatural abundance11
10 mMMoronecidin[15N]-T21G2212
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance12
80 mMCholesterolnatural abundance12
10 mMMoronecidin[15N]-H313
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance13
80 mMCholesterolnatural abundance13
Sample conditionsIonic strength: 40 mM / Label: sample_conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Rennselaer Polytechnic Institute
Bruker AVANCEBrukerAVANCE9002National High Magnetic Field Laboratory
Bruker AVANCEBrukerAVANCE6003National High Magnetic Field Laboratory

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
XwinNMR3.5Bruker Biospincollection
TopSpin2.1Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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