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- PDB-2n53: Solution structure of ovis aries prp -

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Basic information

Entry
Database: PDB / ID: 2n53
TitleSolution structure of ovis aries prp
ComponentsMajor prion protein
KeywordsCELL CYCLE / scrapie / cellular form / transmissible spongiform encephalopathy
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 protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / 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 speciesOvis aries (sheep)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsMunoz, C. / Egalon, A. / Beringue, V. / Rezaei, H. / Dron, M. / Sizun, C.
CitationJournal: J.Virol. / Year: 2016
Title: Generating Bona Fide Mammalian Prions with Internal Deletions.
Authors: Munoz-Montesino, C. / Sizun, C. / Moudjou, M. / Herzog, L. / Reine, F. / Chapuis, J. / Ciric, D. / Igel-Egalon, A. / Laude, H. / Beringue, V. / Rezaei, H. / Dron, M.
History
DepositionJul 6, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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)17,5421
Polymers17,5421
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Major prion protein


Mass: 17541.604 Da / Num. of mol.: 1 / Fragment: PrP residues 103-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: PRNP prion protein, PrP / Variant: VRQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q712V9, UniProt: P23907*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY 20ms
1413D 1H-15N TOCSY 50ms
1512D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.3 mM [U-99% 15N] PrPWT, 10.0 mM Sodium acetate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMPrPWT-1[U-99% 15N]1
10.0 mMSodium acetate-21
Sample conditionsIonic strength: 0 / pH: 5.300 / Pressure: 1.000 atm / Temperature: 298.000 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 950 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2CCPNassignment and nmr data analysis
CYANA3Peter Guntertstructure calculation
TALOS+1Yang Shensecondary structure prediction
TopSpin3.1Brukernmr data processing
CYANA3Peter Guntertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1453 / NOE intraresidue total count: 437 / NOE long range total count: 259 / NOE medium range total count: 283 / NOE sequential total count: 473 / Protein phi angle constraints total count: 90 / Protein psi angle constraints total count: 90
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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