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- PDB-2rmv: Solution structure of synthetic 26-mer peptide containing 142-166... -

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Basic information

Entry
Database: PDB / ID: 2rmv
TitleSolution structure of synthetic 26-mer peptide containing 142-166 sheep prion protein segment and C-terminal cysteine with Y155A mutation
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / tyrosine 155 / synthetic prion peptide / Disease mutation / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Polymorphism
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 / simulated annealing
AuthorsBertho, G. / Bouvier, G. / Hui Bon Hoa, G. / Girault, J.-P.
CitationJournal: To be Published
Title: Key role of the residue 155 in the mechanism of prion transconformation highlighted by the study of sheep mutant peptides
Authors: Bertho, G. / Bouvier, G. / Hui Bon Hoa, G. / Girault, J.-P.
History
DepositionNov 28, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 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)3,3401
Polymers3,3401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Major prion protein / Y14 / PrP / CD230 antigen


Mass: 3339.633 Da / Num. of mol.: 1 / Fragment: residues 142-167 / Mutation: Y155A / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P23907

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 2mM Y14, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: Y14
Sample conditionspH: 6.5 / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500.13 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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