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- PDB-2l1h: Mouse prion protein fragment 121-231 at 20 C -

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Basic information

Entry
Database: PDB / ID: 2l1h
TitleMouse prion protein fragment 121-231 at 20 C
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / prion
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 / lamin binding / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein 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 / lamin binding / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / nucleobase-containing compound metabolic process / 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 / 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 / molecular condensate scaffold activity / terminal bouton / protein destabilization / protein homooligomerization / cellular response to amyloid-beta / 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 / intracellular signal transduction / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / Golgi apparatus / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / 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 / Major Prion Protein / Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / 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
Major prion protein / Major prion protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsChristen, B. / Damberger, F.F. / Perez, D.R. / Hornemann, S. / Wuthrich, K.
CitationJournal: To be Published
Title: Temperature-dependent conformational exchange in the cellular form of prion proteins
Authors: Christen, B. / Damberger, F.F. / Perez, D.R. / Hornemann, S. / Wuthrich, K.
History
DepositionJul 28, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Nov 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 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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)13,4091
Polymers13,4091
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Major prion protein


Mass: 13408.877 Da / Num. of mol.: 1 / Fragment: UNP residues 120-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prnp, RP23-401J24.1-001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4FJQ7, UniProt: P04925*PLUS
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 1H-13C NOESY
NMR detailsText: Two 13C-resolved NOESYs were measured, one with the 13C carrier centered in the aliphatic region and one with the 13C carrier centered in the aromatic region.

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Sample preparation

DetailsContents: 1.0 mM [U-99% 13C; U-99% 15N] protein, 10 mM [U-2H] sodium acetate-2, 0.02 % sodium azide-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity-1[U-99% 13C; U-99% 15N]1
10 mMsodium acetate-2[U-2H]1
0.02 %sodium azide-31
Sample conditionsIonic strength: 0.01 / pH: 4.5 / Pressure: ambient / Temperature: 293.2 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7501
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospinprocessing
XwinNMRBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
ATNOS/CANDID1.2Herrmann, Guntert and Wuthrichchemical shift assignment
ATNOS/CANDID1.2Herrmann, Guntert and Wuthrichpeak picking
DYANA1.0.3Guntert, Mumenthaler and Wuthrichstructure solution
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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