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- PDB-2ktm: Solution NMR structure of H2H3 domain of ovine prion protein (res... -

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Basic information

Entry
Database: PDB / ID: 2ktm
TitleSolution NMR structure of H2H3 domain of ovine prion protein (residues 167-234)
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / H2H3 / Prion Protein / Peptide folding / Fibrilization core / Cell membrane / Membrane / Prion
Function / homology
Function and homology information


side of membrane / tubulin binding / protein homooligomerization / microtubule binding / copper ion binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / 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 protein, beta-ribbon domain / Major Prion Protein / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Major prion protein / Major prion protein
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsPastore, A. / Adrover, M. / Pauwels, K. / de Chiara, C. / Prigent, S. / Rezeai, H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Prion fibrillization is mediated by a native structural element that comprises helices H2 and H3.
Authors: Adrover, M. / Pauwels, K. / Prigent, S. / de Chiara, C. / Xu, Z. / Chapuis, C. / Pastore, A. / Rezaei, H.
History
DepositionFeb 4, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Nov 10, 2021Group: Data collection / Database references
Category: database_2 / 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_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)10,2441
Polymers10,2441
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)12 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major prion protein


Mass: 10244.289 Da / Num. of mol.: 1 / Fragment: H2H3 fragment / Mutation: I208A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Strain: Suffolk / Gene: PRNP / Variant: ARQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q072G4, UniProt: P23907*PLUS
Has protein modificationY

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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 HNCA
1313D HN(CO)CA
1413D 1H-15N NOESY
1513D C(CO)NH
1613D (H)CCH-TOCSY
171CBARO
1812D 1H-1H TOCSY
1912D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.5-0.7 mM [U-100% 13C; U-100% 15N] H2H3-1, 10% D2O-2, 90% H2O-3, 5 mM sodium citrate-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMH2H3-1[U-100% 13C; U-100% 15N]0.5-0.71
10 %D2O-21
90 %H2O-31
5 mMsodium citrate-41
Sample conditionsIonic strength: 0.006 / pH: 3.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIAv2.2Linge, O'Donoghue and Nilgesdata analysis
ARIAv2.2Linge, O'Donoghue and Nilgesstructure solution
ARIAv2.2Linge, O'Donoghue and Nilgesgeometry optimization
ARIAv2.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 12 / Representative conformer: 1

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