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- PDB-6fnv: Solution structure of mule deer prion protein with polymorphism S138 -

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Basic information

Entry
Database: PDB / ID: 6fnv
TitleSolution structure of mule deer prion protein with polymorphism S138
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / prion protein
Function / homology
Function and homology information


side of membrane / protein homooligomerization / copper ion binding / Golgi apparatus / metal ion 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
Major prion protein / Major prion protein
Similarity search - Component
Biological speciesOdocoileus hemionus (mule deer)
MethodSOLUTION NMR / simulated annealing
AuthorsSlapsak, U. / Ilc, G. / Plavec, J.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-424 Slovenia
CitationJournal: To Be Published
Title: Solution structure of mule deer prion protein with polymorphism S138
Authors: Slapsak, U. / Ilc, G. / Plavec, J.
History
DepositionFeb 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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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)16,0091
Polymers16,0091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10900 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2013
RepresentativeModel #113

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Components

#1: Protein Major prion protein / mdPrP(S138)


Mass: 16008.847 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odocoileus hemionus (mule deer) / Gene: prnp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6VS46, UniProt: P47852*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CO)CA
161isotropic13D HNCA
171isotropic13D CBCA(CO)NH
181isotropic13D HN(CA)CB
191isotropic13D HBHA(CO)NH
1101isotropic13D C(CO)NH
1111isotropic13D (H)CCH-TOCSY
1121isotropic13D (H)CCH-TOCSY
1131isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.48 mM [U-99% 13C; U-99% 15N] mdPrP(S138), 20 mM sodium phosphate, 90 % H2O, 10 % [U-2H] D2O, 90% H2O/10% D2O
Label: 13, 15N labeled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.48 mMmdPrP(S138)[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
90 %H2Onatural abundance1
10 %D2O[U-2H]1
Sample conditionsIonic strength: 0 Not defined / Label: mdPrP(S138) / pH: 5.5 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
YASARA NOVAKrieger, E. et alrefinement
CYANA3.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1b18Keller and Wuthrichchemical shift assignment
Sparky3.114Goddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
VNMRVariancollection
PSVSBhattacharya and Montelionedata analysis
CcpNmr AnalysisCCPNdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: 13
NMR ensembleConformer selection criteria: 13 / Conformers calculated total number: 20 / Conformers submitted total number: 20

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