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- PDB-1u3m: NMR structure of the chicken prion protein fragment 128-242 -

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Basic information

Entry
Database: PDB / ID: 1u3m
TitleNMR structure of the chicken prion protein fragment 128-242
Componentsprion-like protein
KeywordsMEMBRANE PROTEIN / PRION PROTEIN / TSE / PRP
Function / homology
Function and homology information


protein insertion into plasma membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / cellular response to xenobiotic stimulus => GO:0071466 / : / : / : / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity ...protein insertion into plasma membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / cellular response to xenobiotic stimulus => GO:0071466 / : / : / : / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of interleukin-2 production / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of amyloid-beta formation / cuprous ion binding / activation of protein kinase activity / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / : / positive regulation of protein targeting to membrane / basement membrane / positive regulation of protein tyrosine kinase activity / synaptic cleft / inclusion body / cellular response to copper ion / neuron projection maintenance / negative regulation of protein phosphorylation / 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 / signaling receptor activity / amyloid-beta binding / microtubule binding / nuclear membrane / response to oxidative stress / protease binding / learning or memory / copper ion binding / membrane raft / dendrite / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / nucleus / 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
Major prion protein homolog
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLysek, D.A. / Calzolai, L. / Guntert, P. / Wuthrich, K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Prion protein NMR structures of chickens, turtles, and frogs
Authors: Calzolai, L. / Lysek, D.A. / Perez, D.R. / Guntert, P. / Wuthrich, K.
History
DepositionJul 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)13,3401
Polymers13,3401
Non-polymers00
Water0
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 #1fewest violations

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Components

#1: Protein prion-like protein / CHPRP


Mass: 13339.875 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: Prnp / Plasmid: pRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P27177

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM chicken prion protein (chPrP(128-242)) U-15N, 13C; 10mM sodium acetate; 95% H2O, 5% D2O; or 99% D2O
Solvent system: 90% H2O, 10% D2O; or 99% D2O
Sample conditionsIonic strength: 10mM / pH: 4.3 / Pressure: ambient / Temperature: 292 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX7503

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Processing

NMR software
NameVersionDeveloperClassification
DYANA6Guentertstructure solution
DYANA6Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 2012 restraints, 1889 are NOE-derived distance constraints, 123 dihedral angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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