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- PDB-1i17: NMR STRUCTURE OF MOUSE DOPPEL 51-157 -

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Basic information

Entry
Database: PDB / ID: 1i17
TitleNMR STRUCTURE OF MOUSE DOPPEL 51-157
ComponentsPRION-LIKE PROTEIN
KeywordsUNKNOWN FUNCTION / mouse doppel / doppel / dpl / prion
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / acrosome reaction / intracellular copper ion homeostasis / single fertilization / protein homooligomerization / copper ion binding / external side of plasma membrane
Similarity search - Function
Prion-like protein Doppel / Prion-like protein Doppel / Prion/Doppel protein, beta-ribbon domain / 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
Prion-like protein doppel
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry molecular dynamics simulated annealing
AuthorsMo, H. / Moore, R.C. / Cohen, F.E. / Westaway, D. / Prusiner, S.B. / Wright, P.E. / Dyson, H.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Two different neurodegenerative diseases caused by proteins with similar structures.
Authors: Mo, H. / Moore, R.C. / Cohen, F.E. / Westaway, D. / Prusiner, S.B. / Wright, P.E. / Dyson, H.J.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Ataxia in Prion Protein (PrP)-Deficient Mice is Associated with Upregulation of the Novel PrP-like Protein Doppel
Authors: Moore, R.C. / Lee, I.Y. / Silverman, G.L. / Harrison, P.M. / Strome, R. / Heinrich, C. / Karunaratne, A. / Pasternak, S.H. / Chishti, M.A. / Liang, Y. / Mastrangelo, P. / Wang, K. / Smit, A. ...Authors: Moore, R.C. / Lee, I.Y. / Silverman, G.L. / Harrison, P.M. / Strome, R. / Heinrich, C. / Karunaratne, A. / Pasternak, S.H. / Chishti, M.A. / Liang, Y. / Mastrangelo, P. / Wang, K. / Smit, A.F. / Katamine, S. / Carlson, G.A. / Cohen, F.E. / Prusiner, S.B. / Melton, D.W. / Tremblay, P. / Hood, L.E. / Westaway, D.
History
DepositionJan 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: PRION-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,2981
Polymers12,2981
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 / 100structures with the least restraint violations
RepresentativeModel #16lowest energy

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Components

#1: Protein PRION-LIKE PROTEIN / MOUSE DOPPEL


Mass: 12297.794 Da / Num. of mol.: 1 / Fragment: GLOBULAR DOMAIN (RESIDUES 51-157)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET21A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9QUG3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 4mM 15N or 2mM 15N/13C protein 20mM d3-NaOAc, pH5.2
Solvent system: D2O:H2O = 1:9
Sample conditionsIonic strength: 0.02M / pH: 5.2 / Pressure: 1 atm / Temperature: 299 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
Amber7Caserefinement
RefinementMethod: distance geometry molecular dynamics simulated annealing
Software ordinal: 1 / Details: based on 1311 distance restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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