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- PDB-1s4t: Solution structure of synthetic 21mer peptide spanning region 135... -

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Basic information

Entry
Database: PDB / ID: 1s4t
TitleSolution structure of synthetic 21mer peptide spanning region 135-155 (in human numbering) of sheep prion protein
ComponentsMajor prion protein
KeywordsUNKNOWN FUNCTION / prion / helix
Function / homology
Function and homology information


side of membrane / tubulin binding / protein homooligomerization / microtubule binding / copper ion binding / Golgi apparatus / identical protein binding / plasma membrane
Similarity search - Function
Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
MethodSOLUTION NMR / Molecular dynamics with AMBER99 all-atom force field parameters by using the variable target function approach in the torsion angle space with the standard geometry of amino acids, peptide bonds.
AuthorsKozin, S.A. / Lepage, C. / Hui Bon Hoa, G. / Rabesona, H. / Mazur, A.K. / Blond, A. / Cheminant, M. / Haertle, T. / Debey, P. / Rebuffat, S.
CitationJournal: To be Published
Title: Specific recognition between surface loop 2 (132-143) and helix 1 (144-154) within sheep prion protein from in vitro studies of synthetic peptides
Authors: Kozin, S.A. / Lepage, C. / Hui Bon Hoa, G. / Rabesona, H. / Mazur, A.K. / Blond, A. / Cheminant, M. / Haertle, T. / Debey, P. / Rebuffat, S.
History
DepositionJan 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: Major prion protein


Theoretical massNumber of molelcules
Total (without water)2,7431
Polymers2,7431
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 / 1000The submitted conformer models are the 20 structures with the least restraint violations and the lowestt energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Major prion protein / PrP


Mass: 2742.977 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide has been chemically synthesized. The sequence occurs naturally in sheep.
References: UniProt: P23907

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 5 mM / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: nd / pH: 2.3 / Pressure: ambient / Temperature: 324 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukercollection
AURELIA2.5.9Brukerprocessing
ICMDy2.3Mazur, A.K.structure solution
ICMDy2.3Mazur, A.K.refinement
RefinementMethod: Molecular dynamics with AMBER99 all-atom force field parameters by using the variable target function approach in the torsion angle space with the standard geometry of amino acids, peptide bonds.
Software ordinal: 1
Details: The structures are based on a total of 134 NOE-derived distance constraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the least restraint violations and the lowestt energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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