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- PDB-2kfm: Mouse Prion Protein (121-231) with Mutations Y225A and Y226A -

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Basic information

Entry
Database: PDB / ID: 2kfm
TitleMouse Prion Protein (121-231) with Mutations Y225A and Y226A
ComponentsMajor prion protein
KeywordsUNKNOWN FUNCTION / Mouse Prion Protein / Mutation Y225A / Y226A / long-range effect / Cell membrane / Glycoprotein / Golgi apparatus / GPI-anchor / Hydroxylation / Lipoprotein / Membrane / Polymorphism / Prion / MEMBRANE PROTEIN
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / positive regulation of glutamate receptor signaling pathway / lamin binding / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / ATP-dependent protein binding / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / positive regulation of glutamate receptor signaling pathway / lamin binding / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / ATP-dependent protein binding / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / cupric ion binding / nucleobase-containing compound metabolic process / activation of protein kinase activity / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / intracellular copper ion homeostasis / regulation of peptidyl-tyrosine phosphorylation / negative regulation of protein phosphorylation / response to cadmium ion / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / negative regulation of DNA-binding transcription factor activity / molecular condensate scaffold activity / protein destabilization / terminal bouton / protein homooligomerization / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / regulation of protein localization / amyloid-beta binding / protein-folding chaperone binding / protease binding / microtubule binding / nuclear membrane / molecular adaptor activity / response to oxidative stress / transmembrane transporter binding / learning or memory / postsynaptic density / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
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 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsChristen, B. / Hornemann, S. / Damberger, F.F. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Prion Protein NMR Structure from Tammar Wallaby (Macropus eugenii) Shows that the beta2-alpha2 Loop Is Modulated by Long-Range Sequence Effects.
Authors: Christen, B. / Hornemann, S. / Damberger, F.F. / Wuthrich, K.
History
DepositionFeb 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_assembly ...pdbx_database_related / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_related.db_id
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)13,2251
Polymers13,2251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6920 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80
RepresentativeModel #1fewest violations

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Components

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


Mass: 13224.684 Da / Num. of mol.: 1 / Mutation: Y225A,Y226A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prnp, Prn-p, Prp / Production host: Escherichia coli (E. coli) / References: UniProt: P04925
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HNCA
1413D CBCA(CO)NH
1513D 1H-15N TOCSY
1613D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 10 mM [U-100% 2H] sodium acetate-1, 2 mM [U-99% 13C; U-99% 15N] entity-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium acetate-1[U-100% 2H]1
2 mMentity-2[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 0.01 / pH: 4.5 / Pressure: ambient / Temperature: 293.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX7503
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichdata analysis
ATNOS/CANDID1.2Herrmann, Guntert and Wuthrichpeak picking
ATNOS/CANDID1.2Herrmann, Guntert and Wuthrichchemical shift assignment
DYANA1.0.3Guntert, Mumenthaler and Wuthrichstructure solution
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformers calculated total number: 80 / Conformers submitted total number: 20

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