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- PDB-2m1j: Ovine Doppel Signal peptide (1-30) -

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Basic information

Entry
Database: PDB / ID: 2m1j
TitleOvine Doppel Signal peptide (1-30)
ComponentsPrion-like protein doppel
KeywordsUNKNOWN FUNCTION / Prion-like protein
Function / homology
Function and homology information


: / acrosome reaction / protein homooligomerization / copper ion binding
Similarity search - Function
Prion-like protein Doppel / Prion-like protein Doppel / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
Prion-like protein doppel
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model6
AuthorsPimenta, J. / Viegas, A. / Sardinha, J. / Santos, A. / Cantante, C. / Dias, F.M.V. / Soares, R. / Cabrita, E.J. / Fontes, C.M.G.A. / Prates, J.A.M. / Pereira, R.M.L.N.
CitationJournal: Peptides / Year: 2013
Title: NMR solution structure and SRP54M predicted interaction of the N-terminal sequence (1-30) of the ovine Doppel protein.
Authors: Pimenta, J. / Viegas, A. / Sardinha, J. / Martins, I.C. / Cabrita, E.J. / Fontes, C.M. / Prates, J.A. / Pereira, R.M.
History
DepositionNov 28, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 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: Prion-like protein doppel


Theoretical massNumber of molelcules
Total (without water)3,3211
Polymers3,3211
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 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Prion-like protein doppel / PrPLP


Mass: 3321.125 Da / Num. of mol.: 1 / Fragment: signal peptide (UNP residues 1-30) / Source method: obtained synthetically / Source: (synth.) Ovis aries (sheep) / References: UniProt: Q9GJY2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 100 mM DHPC, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 100 mM / Component: DHPC-1
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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