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- PDB-1m25: STRUCTURE OF SYNTHETIC 26-MER PEPTIDE CONTAINING 145-169 SHEEP PR... -

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Basic information

Entry
Database: PDB / ID: 1m25
TitleSTRUCTURE OF SYNTHETIC 26-MER PEPTIDE CONTAINING 145-169 SHEEP PRION PROTEIN SEGMENT AND C-TERMINAL CYSTEINE IN TFE SOLUTION
ComponentsMAJOR PRION PROTEIN
KeywordsUNKNOWN FUNCTION / helix / prion / TFE
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
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / 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 / simulated annealing using torsion angle dynamics as implemented in the program CNS
AuthorsMegy, S. / Bertho, G. / Kozin, S.A. / Coadou, G. / Debey, P. / Hoa, G.H. / Girault, J.-P.
Citation
Journal: Protein Sci. / Year: 2004
Title: Possible role of region 152-156 in the structural duality of a peptide fragment from sheep prion protein
Authors: Megy, S. / Bertho, G. / Kozin, S.A. / Debey, P. / Hoa, G.H. / Girault, J.-P.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Sheep prion protein synthetic peptide spanning helix 1 and beta-strand 2 (residues 142-166) shows beta-hairpin structure in solution
Authors: Kozin, S.A. / Bertho, G. / Mazur, A.K. / Rabesona, H. / Girault, J.-P. / Haertle, T. / Takahashi, M. / Debey, P. / Hoa, G.H.
History
DepositionJun 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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)3,4321
Polymers3,4321
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 / 200back calculated data agree with experimental NOESY spectrum,structures with the lowest energy
RepresentativeModel #2lowest energy, without noe violations

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Components

#1: Protein/peptide MAJOR PRION PROTEIN / PrP


Mass: 3431.729 Da / Num. of mol.: 1 / Fragment: Residues 145-169 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. EXCEPT FOR THE C-TERMINAL CYSTEINE, THIS SEQUENCE OCCURS NATURALLY IN OVIS ARIES (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: 4.5mM
Solvent system: 87/13 (v/v), CF3CD2OH / 10mM sodium phosphate buffer, pH 6.5
Sample conditionsIonic strength: 1mM / pH: 6.5 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
CNS0.9Brungerrefinement
CNS0.9Brungerstructure solution
RefinementMethod: simulated annealing using torsion angle dynamics as implemented in the program CNS
Software ordinal: 1
Details: the structures are based on a total of 252 interresidual NOE-derived distance constraints, 22 dihedral angle restraints, 25 CSI restraints from Ha, Ca, Cb.
NMR representativeSelection criteria: lowest energy, without noe violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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