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- PDB-5l6r: PrP226* - Solution-state NMR structure of truncated human prion p... -

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Basic information

Entry
Database: PDB / ID: 5l6r
TitlePrP226* - Solution-state NMR structure of truncated human prion protein
ComponentsMajor prion protein
KeywordsTRANSPORT PROTEIN / TRUNCATED FORM OF HUMAN PRION PROTEIN / BINDS TO mAb V5B2 / STRUCTURE FROM CYANA 3.0
Function / homology
Function and homology information


positive regulation of glutamate receptor signaling pathway / 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 / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions ...positive regulation of glutamate receptor signaling pathway / 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 / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of protein processing / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of interleukin-2 production / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / tubulin binding / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / negative regulation of DNA-binding transcription factor activity / 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 / protein-folding chaperone binding / signaling receptor activity / amyloid-beta binding / microtubule binding / protease binding / nuclear membrane / postsynapse / transmembrane transporter binding / response to oxidative stress / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / 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
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsKovac, V. / Zupancic, B. / Ilc, G. / Curin Serbec, V. / Plavec, J.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyP4-0176 Slovenia
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Truncated prion protein PrP226* - A structural view on its role in amyloid disease.
Authors: Kovac, V. / Zupancic, B. / Ilc, G. / Plavec, J. / Curin Serbec, V.
History
DepositionMay 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Oct 16, 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 / _database_2.pdbx_database_accession

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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)16,5951
Polymers16,5951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11600 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

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


Mass: 16595.449 Da / Num. of mol.: 1 / Fragment: UNP residues 90-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRNP, ALTPRP, PRIP, PRP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04156
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
141isotropic12D 1H-15N HSQC
1151isotropic12D 1H-15N HSQC NH2 only
1101isotropic13D HN(CA)CB
1141isotropic13D HBHA(CO)NH
1121isotropic13D 1H-15N NOESY
171isotropic13D CBCA(CO)NH
111isotropic13D HNCO
121isotropic13D HNCA
1161isotropic13D HN(CO)CA
151isotropic12D 1H-13C HSQC aliphatic
181isotropic12D 1H-13C HSQC aromatic
191isotropic13D 1H-13C NOESY aliphatic
161isotropic13D 1H-13C NOESY aromatic
1131isotropic13D CCH-TOCSY
1111isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
Label: NH_detection / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.9 mM / Component: PrP226* / Isotopic labeling: (13C, 15N)-doubly labeled
Sample conditionsIonic strength: 150 mM / Label: NH_conditions / pH: 4.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOSCornilescu, Delaglio and Baxgeometry optimization
YASARAProf. Dr. Gregor Hoegenauer, Prof. Dr. Guenther Koraimann, Prof. Dr. Andreas Kungl, Prof. Dr. Gert Vriendrefinement
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
UCSF ChimeraResource for Biocomputing, Visualization, and Informaticsdata analysis
NMR ensembleConformers submitted total number: 20

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