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- PDB-8b4r: Antimicrobial peptide capitellacin from polychaeta Capitella tele... -

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Basic information

Entry
Database: PDB / ID: 8b4r
TitleAntimicrobial peptide capitellacin from polychaeta Capitella teleta in DPC (dodecylphosphocholine) micelles, monomeric form
ComponentsBRICHOS domain-containing protein
KeywordsANTIMICROBIAL PROTEIN / PROTEIN / BETA-HAIRPIN / MONOMER
Function / homologyBRICHOS domain / BRICHOS domain profile. / membrane / BRICHOS domain-containing protein
Function and homology information
Biological speciesCapitella teleta (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsMironov, P.A. / Reznikova, O.V. / Paramonov, A.S. / Shenkarev, Z.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Education and Science of the Russian Federation075-15-2021-1049 Russian Federation
CitationJournal: Biomolecules / Year: 2024
Title: Dimerization of the beta-Hairpin Membrane-Active Cationic Antimicrobial Peptide Capitellacin from Marine Polychaeta: An NMR Structural and Thermodynamic Study.
Authors: Mironov, P.A. / Paramonov, A.S. / Reznikova, O.V. / Safronova, V.N. / Panteleev, P.V. / Bolosov, I.A. / Ovchinnikova, T.V. / Shenkarev, Z.O.
History
DepositionSep 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 13, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRICHOS domain-containing protein


Theoretical massNumber of molelcules
Total (without water)2,3891
Polymers2,3891
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 / 200structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein/peptide BRICHOS domain-containing protein


Mass: 2388.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capitella teleta (invertebrata) / Gene: CAPTEDRAFT_185237 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R7TSD6
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
112anisotropic22D NOESY
122anisotropic22D TOCSY
132anisotropic22D 1H-13C HSQC aliphatic
142anisotropic22D 1H-13C HSQC aromatic
151anisotropic13D 1H-15N NOESY
161anisotropic13D (H)CCH-TOCSY
171anisotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle10.07 mM [U-15N] capitellacin, 5 % [U-99% 2H] D2O, 14 mM DPC, 95% H2O/5% D2OThe peptide:detergent ratio of 1:20015N_sample95% H2O/5% D2O
micelle20.84 mM capitellacin, 10 % [U-99% 2H] D2O, 100 % water, 168 mM DPC, 95% H2O/5% D2OThe peptide:detergent ratio of 1:100natural_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.07 mMcapitellacin[U-15N]1
5 %D2O[U-99% 2H]1
14 mMDPCnatural abundance1
0.84 mMcapitellacinnatural abundance2
10 %D2O[U-99% 2H]2
100 %waternatural abundance2
168 mMDPCnatural abundance2
Sample conditionsIonic strength: 0.001 M / Label: condition_1 / pH: 5.4 / Pressure: AMBIENT Pa / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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