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- PDB-1skh: N-terminal (1-30) of bovine Prion protein -

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Basic information

Entry
Database: PDB / ID: 1skh
TitleN-terminal (1-30) of bovine Prion protein
ComponentsMajor prion protein 2
KeywordsUNKNOWN FUNCTION / coil-helix-coil
Function / homology
Function and homology information


positive regulation of glutamate receptor signaling pathway / cuprous ion binding / side of membrane / inclusion body / cellular response to copper ion / positive regulation of calcium-mediated signaling / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to amyloid-beta ...positive regulation of glutamate receptor signaling pathway / cuprous ion binding / side of membrane / inclusion body / cellular response to copper ion / positive regulation of calcium-mediated signaling / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / amyloid-beta binding / microtubule binding / G-quadruplex RNA binding / nuclear membrane / membrane raft / copper ion binding / dendrite / protein-containing complex binding / cell surface / Golgi apparatus / identical protein binding / plasma membrane / cytosol
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
Major prion protein / Major prion protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / DYANA torsion angle dynamics, simulated annealing
AuthorsBiverstahl, H. / Andersson, A. / Graslund, A. / Maler, L.
CitationJournal: Biochemistry / Year: 2004
Title: NMR solution structure and membrane interaction of the N-terminal sequence (1-30) of the bovine prion protein.
Authors: Biverstahl, H. / Andersson, A. / Graslund, A. / Maler, L.
History
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: 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_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 2


Theoretical massNumber of molelcules
Total (without water)3,4241
Polymers3,4241
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)22 / 60a combination of least constraint violations and DYANA target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Major prion protein 2 / PrP / Major scrapie-associated fibril protein 2


Mass: 3424.280 Da / Num. of mol.: 1 / Fragment: N-terminal domain (residues 1-30) / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q01880, UniProt: P10279*PLUS

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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: 1 mM bovine PrP, 100 mM dihexanoyl-sn-glycero-3-phosphatidylcholine-d22 (DHPC), H2O, D2O
Solvent system: 100 mM dihexanoyl-sn-glycero-3-phosphatidylcholine-d22 (DHPC), H2O, D2O
Sample conditionspH: 3.4 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionClassification
Felixdata analysis
VNMR6.1ccollection
DYANA1.5structure solution
DYANA1.5refinement
RefinementMethod: DYANA torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: a combination of least constraint violations and DYANA target function
Conformers calculated total number: 60 / Conformers submitted total number: 22

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