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- PDB-2mv8: Solution structure of Ovis Aries PrP with mutation delta190-197 -

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Basic information

Entry
Database: PDB / ID: 2mv8
TitleSolution structure of Ovis Aries PrP with mutation delta190-197
ComponentsMajor prion protein
KeywordsIMMUNE SYSTEM / prion / scrapie / major prion protein / 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/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
Major prion protein / Major prion protein
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model10
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
DepositionSep 25, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Aug 17, 2016Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_conn_type / 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

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Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)16,6701
Polymers16,6701
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 #1closest to the average

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Components

#1: Protein Major prion protein


Mass: 16669.625 Da / Num. of mol.: 1 / Fragment: 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 HNCO
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D 1H-15N NOESY
1722D 1H-1H NOESY
1822D 1H-15N HSQC
1912D 1H-13C HSQC
11013D (H)CCH-TOCSY
11132D 1H-13C HSQC
11233D (H)CCH-TOCSY
11332D 1H-1H NOESY
11432D 1H-13C HSQC
11533D aromatic (H)CCH-TOCSY
11633D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.35 mM [U-99% 13C; U-99% 15N] PrPdelta190, 10.00 mM Sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
20.45 mM [U-99% 15N] PrPdelta190, 10.00 mM Sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
30.35 mM [U-99% 13C; U-99% 15N] PrPdelta190, 10.00 mM Sodium acetate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMPrPdelta190-197-1[U-99% 13C; U-99% 15N]1
10.00 mMSodium acetate-21
0.45 mMPrPdelta190-197-3[U-99% 15N]2
10.00 mMSodium acetate-42
0.35 mMPrPdelta190-197-5[U-99% 13C; U-99% 15N]3
10.00 mMSodium acetate-63
Sample conditionsIonic strength: 0 / pH: 5.3 / Pressure: 1.00 atm / Temperature: 298.00 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Peter Guntertstructure calculation
CcpNmr Analysis2.2CCPNassignment
TALOS+1Yang Shendihedral angles
TopSpin3.1Brukercollection
TopSpin3.1Brukerprocessing
CYANAPeter Guntertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1938 / NOE intraresidue total count: 536 / NOE long range total count: 465 / NOE medium range total count: 383 / NOE sequential total count: 553 / Protein phi angle constraints total count: 77 / Protein psi angle constraints total count: 79
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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