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- PDB-2fj3: NMR solution of rabbit Prion Protein (91-228) -

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Basic information

Entry
Database: PDB / ID: 2fj3
TitleNMR solution of rabbit Prion Protein (91-228)
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / prion protein
Function / homology
Function and homology information


regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade ...regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / negative regulation of type II interferon production / positive regulation of protein targeting to membrane / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / terminal bouton / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / microtubule binding / protease binding / nuclear membrane / response to oxidative stress / learning or memory / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat / Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein ...Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat / Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / 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 speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / simulated annealing
AuthorsLi, J. / Lin, D.H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Unique structural characteristics of the rabbit prion protein
Authors: Wen, Y. / Li, J. / Yao, W. / Xiong, M. / Hong, J. / Peng, Y. / Xiao, G. / Lin, D.H.
History
DepositionDec 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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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)15,6571
Polymers15,6571
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)15 / 200structures with the lowest energ
RepresentativeModel #1lowest energy

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Components

#1: Protein Major prion protein / protein(prion protein) / PrP / PrP27-30 / PrP33-35C


Mass: 15657.441 Da / Num. of mol.: 1 / Fragment: Residues 91-228
Source method: isolated from a genetically manipulated source
Details: The region of residues 91-123 is loop and the structure domain is residues 124-228.
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pET30(+)a / Cellular location (production host): Cytoplasm / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95211
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA-J
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM PrP U-15N,13C; 20mM acetate buffer (pH 4.5); 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglioprocessing
ARIA1.2Niglesstructure solution
ARIA1.2Niglesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energ
Conformers calculated total number: 200 / Conformers submitted total number: 15

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