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- PDB-2pco: Spatial Structure and Membrane Permeabilization for Latarcin-1, a... -

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Basic information

Entry
Database: PDB / ID: 2pco
TitleSpatial Structure and Membrane Permeabilization for Latarcin-1, a Spider Antimicrobial Peptide
ComponentsLatarcin-1
KeywordsTOXIN / continuous helix
Function / homologyLatarcin precursor / Latarcin precursor / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / M-zodatoxin-Lt1a
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDubovskii, P.V. / Volynsky, P.E. / Polyansky, A.A. / Chupin, V.V. / Efremov, R.G. / Arseniev, A.S.
CitationJournal: Biochemistry / Year: 2008
Title: Three-dimensional structure/hydrophobicity of latarcins specifies their mode of membrane activity.
Authors: Dubovskii, P.V. / Volynsky, P.E. / Polyansky, A.A. / Karpunin, D.V. / Chupin, V.V. / Efremov, R.G. / Arseniev, A.S.
History
DepositionMar 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Latarcin-1


Theoretical massNumber of molelcules
Total (without water)3,2131
Polymers3,2131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Latarcin-1 / Ltc-1


Mass: 3213.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in spider (Lachesana tarabaevi) venom.
References: UniProt: Q1ELT9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1322D NOESY
142DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM Ltc1, 120 mM perdeuterated SDS, pH 7.1, salt-free, 90% H2O, 10% D2O90% H2O/10% D2O
22 mM Ltc1, 120 mM perdeuterated SDS, pH 7.1, salt-free, 100% D2O100% D2O
Sample conditionsIonic strength: salt-free / pH: 7.1 / Pressure: ambient / Temperature: 318 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6.Guentert P.refinement
XwinNMR3.1.aBRUKERcollection
XEASY40300000Xia & Bartelsdata analysis
FANMEM4.1Nolde, Arseniev, Vergoten, Efremovrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: In total, 146 distance and 127 torsion angle constraints were used
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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