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- PDB-1fkc: HUMAN PRION PROTEIN (MUTANT E200K) FRAGMENT 90-231 -

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Basic information

Entry
Database: PDB / ID: 1fkc
TitleHUMAN PRION PROTEIN (MUTANT E200K) FRAGMENT 90-231
ComponentsPRION PROTEINPRNP
KeywordsMEMBRANE PROTEIN / three helix / CREUTZFELDT-JAKOB DISEASE / PRION / AGGREGATION
Function / homology
Function and homology information


: / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / NCAM1 interactions / negative regulation of interleukin-17 production / ATP-dependent protein binding ...: / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / NCAM1 interactions / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of interleukin-2 production / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / negative regulation of amyloid-beta formation / cuprous ion binding / negative regulation of activated T cell proliferation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / negative regulation of type II interferon production / : / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / positive regulation of protein tyrosine kinase activity / response to cadmium ion / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / molecular condensate scaffold activity / neuron projection maintenance / tubulin binding / protein sequestering activity / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / postsynapse / nuclear membrane / response to oxidative stress / protease binding / transmembrane transporter binding / postsynaptic density / learning or memory / molecular adaptor activity / regulation of cell cycle / cell cycle / copper ion binding / membrane raft / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsZhang, Y. / Swietnicki, W. / Zagorski, M.G. / Surewicz, W.K. / Soennichsen, F.D.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Solution structure of the E200K variant of human prion protein. Implications for the mechanism of pathogenesis in familial prion diseases.
Authors: Zhang, Y. / Swietnicki, W. / Zagorski, M.G. / Surewicz, W.K. / Sonnichsen, F.D.
History
DepositionAug 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

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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)16,1691
Polymers16,1691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 60structures with the lowest energy
RepresentativeModel #11lowest energy

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Components

#1: Protein PRION PROTEIN / PRNP


Mass: 16169.063 Da / Num. of mol.: 1 / Fragment: PRP(90-231) / Mutation: E200K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: BRAIN / Organ: BRAIN / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: P04156

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2223D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.8 mM E200K(90-231)PrP U-15N,13C; 10mM acetate buffer
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.00001 / pH: 4.6 / 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 DRXBrukerDRX8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS0.9Brungerstructure solution
ARIA0.9Niglesstructure solution
CNS0.9Brungerrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 1

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