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- PDB-2k56: Bank Vole Prion Protein (121-231) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2k56
TitleBank Vole Prion Protein (121-231)
ComponentsMajor prion protein
KeywordsUNKNOWN FUNCTION / Prion Protein / Membrane
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / 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 protein, beta-ribbon domain / Major Prion Protein / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMyodes glareolus (Bank vole)
MethodSOLUTION NMR / OPAL (water shell), TORSION ANGLE DYNAMICS,
AuthorsChristen, B. / Hornemann, S. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: NMR Structure of the Bank Vole Prion Protein at 20 degrees C Contains a Structured Loop of Residues 165-171.
Authors: Christen, B. / Perez, D.R. / Hornemann, S. / Wuthrich, K.
History
DepositionJun 26, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)13,2441
Polymers13,2441
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Major prion protein


Mass: 13243.665 Da / Num. of mol.: 1 / Fragment: UNP residues 121-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myodes glareolus (Bank vole) / Gene: PrP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VHV5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 15N] Prion Protein, 10 % D2O, 90 % H2O, 10 mM [U-2H] sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] Prion Protein, 10 % D2O, 90 % H2O, 10 mM [U-2H] sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPrion Protein[U-99% 15N]1
10 %D2O1
90 %H2O1
10 mMsodium acetate[U-2H]1
1 mMPrion Protein[U-99% 13C; U-99% 15N]2
10 %D2O2
90 %H2O2
10 mMsodium acetate[U-2H]2
Sample conditionsIonic strength: 0.01 / pH: 4.5 / Pressure: ambient / Temperature: 293.2 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7501
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
OPAL1.2Luginbuhl, Guntert, Billeter and Wuthrichrefinement
CARA1.5.5Keller, R.data analysis
ATNOS/CANDID1.2Herrmann, Guntert and Wuthrichpeak picking
ATNOS/CANDID1.2Herrmann, Guntert and Wuthrichchemical shift assignment
DYANA1.0.3Guntert, Braun and Wuthrichstructure solution
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
XwinNMRBruker Biospincollection
RefinementMethod: OPAL (water shell), TORSION ANGLE DYNAMICS, / Software ordinal: 1
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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