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- PDB-6ena: Nemertide alpha-1 -

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Basic information

Entry
Database: PDB / ID: 6ena
TitleNemertide alpha-1
ComponentsNemertide alpha-1
KeywordsTOXIN / Nemertea / Lineus Longissimus / inhibitor cystine knot
Function / homologyOmega-conotoxin family signature. / sodium channel regulator activity / toxin activity / extracellular region / Nemertide alpha-1
Function and homology information
Biological speciesLineus longissimus (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsJacobsson, E. / Rosengren, K.J. / Goransson, U.
Funding support Sweden, Australia, 2items
OrganizationGrant numberCountry
Swedish Research Council2014-3327 Sweden
Australian Research CouncilFT130100890 Australia
CitationJournal: Sci Rep / Year: 2018
Title: Lineus longissimus, the longest animal on earth, expresses peptide toxins targeting voltage gated sodium channels
Authors: Jacobsson, E. / Andersson, H.S. / Strand, M. / Peigneur, S. / Eriksson, C. / Loden, H. / Shariatgorji, M. / Andren, P.E. / Lebbe, K.M. / Rosengren, K.J. / Tytgat, J. / Goransson, U.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nemertide alpha-1


Theoretical massNumber of molelcules
Total (without water)3,3191
Polymers3,3191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2430 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50lowest MolProbity score
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Nemertide alpha-1


Mass: 3318.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lineus longissimus (invertebrata) / References: UniProt: A0A384E137*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
211isotropic12D 1H-1H NOESY
322isotropic12D 1H-13C HSQC
231isotropic12D 1H-15N HSQC
241isotropic12D 1H-1H TOCSY
352isotropic12D 1H-1H TOCSY
362isotropic12D 1H-1H NOESY
372isotropic12D 1H-1H ECOSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution13 mg/mL Nemertide alpha-1, 90% H2O/10% D2ONermertide alpha-1 (H2O)90% H2O/10% D2O
solution23 mg/mL Nemertide alpha-1, 100% D2ONemertide alpha-1 (D2O)100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mg/mLNemertide alpha-1natural abundance1
3 mg/mLNemertide alpha-1natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
20 mMH2O4.10.1ambient atm298 K
30 mMD2O4.10.2ambient atm298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TopSpin2.1Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Initial structures were calculated using torsion angle dynamics and the structures were subsequently refined and energy minimised using cartesian dynamics in explicit solvent. Protocols from ...Details: Initial structures were calculated using torsion angle dynamics and the structures were subsequently refined and energy minimised using cartesian dynamics in explicit solvent. Protocols from the RECOORD data base were used.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest MolProbity score / Conformers calculated total number: 50 / Conformers submitted total number: 20

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