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- PDB-1z65: Mouse Doppel 1-30 peptide -

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Basic information

Entry
Database: PDB / ID: 1z65
TitleMouse Doppel 1-30 peptide
ComponentsPrion-like protein doppel
KeywordsUNKNOWN FUNCTION / transmembrane helix / DHPC / mouse Doppel
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / acrosome reaction / single fertilization / intracellular copper ion homeostasis / protein homooligomerization / copper ion binding / external side of plasma membrane
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
MethodSOLUTION NMR
AuthorsPapadopoulos, E.
CitationJournal: Biochemistry / Year: 2006
Title: NMR Solution Structure of the Peptide Fragment 1-30, Derived from Unprocessed Mouse Doppel Protein, in DHPC Micelles
Authors: Papadopoulos, E. / Oglecka, K. / Maler, L. / Jarvet, J. / Wright, P.E. / Dyson, H.J. / Graslund, A.
History
DepositionMar 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4May 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: Prion-like protein doppel


Theoretical massNumber of molelcules
Total (without water)3,4041
Polymers3,4041
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 50structures with favorable non-bond energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 3404.213 Da / Num. of mol.: 1 / Fragment: residues 1-30 / Source method: obtained synthetically
Details: sequence appears naturally in Mus musculus, gene Prnd
References: UniProt: Q9QUG3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 2 mM mouse Doppel 1-30 peptide / Solvent system: 100mM DHPC, 10% D2O
Sample conditionsIonic strength: unknown / pH: 3.5 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionClassification
Felix2000.1data analysis
DYANA1.5structure solution
DYANA1.5refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 50 / Conformers submitted total number: 22

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