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- PDB-1dx1: BOVINE PRION PROTEIN RESIDUES 23-230 -

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Basic information

Entry
Database: PDB / ID: 1dx1
TitleBOVINE PRION PROTEIN RESIDUES 23-230
ComponentsPRION PROTEIN
KeywordsPROTEIN FIBRIL / PRION PROTEIN / REPEAT STRUCTURE
Function / homology
Function and homology information


type 5 metabotropic glutamate receptor binding / cuprous ion binding / : / side of membrane / inclusion body / cellular response to copper ion / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to amyloid-beta ...type 5 metabotropic glutamate receptor binding / cuprous ion binding / : / side of membrane / inclusion body / cellular response to copper ion / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / amyloid-beta binding / G-quadruplex RNA binding / microtubule binding / nuclear membrane / membrane raft / copper ion binding / dendrite / protein-containing complex binding / Golgi apparatus / cell surface / identical protein binding / plasma membrane / cytosol
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 speciesBOS TAURUS (cattle)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLopez Garcia, F. / Zahn, R. / Riek, R. / Billeter, M. / Wuthrich, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: NMR Structure of the Bovine Prion Protein
Authors: Lopez-Garcia, F. / Zahn, R. / Riek, R. / Wuthrich, K.
History
DepositionDec 15, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Aug 5, 2015Group: Database references / Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRION PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,6461
Polymers23,6461
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 / 50LEAST RESTRAINT VIOLATION
RepresentativeModel #3

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Components

#1: Protein PRION PROTEIN / PRP / MAJOR PRION PROTEIN


Mass: 23645.928 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Cellular location: EXTRACELLULAR / Gene: PRNP / Organ: BRAIN / Plasmid: PRSET A / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10279
Compound detailsTHE PDB ENTRIES 1DWY, 1DWZ, 1DX0 AND 1DX1 FORM A SET OF STRUCTURE DETERMINATIONS AS: 1DWY THE ...THE PDB ENTRIES 1DWY, 1DWZ, 1DX0 AND 1DX1 FORM A SET OF STRUCTURE DETERMINATIONS AS: 1DWY THE MINIMIZED CONFORMER CLOSEST TO THE MEAN OF THE FRAGMENT BPRP(121-230) (ONLY SUBMITTED RESIDUES 124-227) 1DWZ 20 MINIMIZED CONFORMERS OF THE FRAGMENT BPRP(121-230) (ONLY SUBMITTED RESIDUES 124-227) 1DX0 THE MINIMIZED CONFORMER CLOSEST TO THE MEAN OF THE FULL LENGTH BPRP(23-230) (ONLY SUBMITTED RESIDUES 124-227) 1DX1 20 MINIMIZED CONFORMERS OF THE FULL LENGTH BPRP(23-230) (ONLY SUBMITTED RESIDUES 124-227) THE SEQUENCE NUMBERING GIVEN IN THESE ENTRIES IS THAT FOR HUMAN PRION PROTEIN (RATHER THAN SEQUENTIAL) BASED ON SEQUENCE ALIGNMENT.
Sequence detailsRESIDUES (GLY SER) INSERTED AT THE N-TERMINUS GLY A 21 CLONING ARTIFACT SER A 22 CLONING ARTIFACT

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
NMR detailsText: CLOSEST TO THE MEAN (BACKBONE HEAVY ATOMS OF RESIDUES 125-227). THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 0.01 / pH: 4.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
OPALPKORADI, BILLETER,GUNTERTrefinement
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 20

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