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- PDB-1h0l: HUMAN PRION PROTEIN 121-230 M166C/E221C -

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Basic information

Entry
Database: PDB / ID: 1h0l
TitleHUMAN PRION PROTEIN 121-230 M166C/E221C
ComponentsMAJOR PRION PROTEIN
KeywordsCELL CYCLE / BRAIN / GLYCOPROTEIN / GPI-ANCHOR / POLYMORPHISM / DISEASE MUTATION
Function / homology
Function and homology information


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 / NCAM1 interactions / type 5 metabotropic glutamate receptor binding ...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 / NCAM1 interactions / 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 / negative regulation of protein processing / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of interleukin-2 production / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / long-term memory / regulation of peptidyl-tyrosine phosphorylation / negative regulation of protein phosphorylation / response to cadmium ion / inclusion body / cellular response to copper ion / neuron projection maintenance / tubulin binding / 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 / 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 / regulation of cell cycle / postsynapse / postsynaptic density / 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
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 speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZahn, R. / Guntert, P. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: NMR Structure of a Variant Human Prion Protein with Two Disulfide Bridges
Authors: Zahn, R. / Guntert, P. / Von Schroetter, C. / Wuthrich, K.
History
DepositionJun 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)13,1071
Polymers13,1071
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 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #2

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Components

#1: Protein MAJOR PRION PROTEIN / PRP / PRION PROTEIN / PRP27-30 / PRP33-35C


Mass: 13106.572 Da / Num. of mol.: 1 / Fragment: RESIDUES 121-230 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN / Plasmid: PRSET A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04156
Compound detailsDISULFIDE BOND BETWEEN C166 AND C221 ENGINEERED MUTATION MET 166 CYS AND GLU 221 CYS CHAIN A
Has protein modificationY
Sequence details2 RESIDUES (GLY SER) INSERTED AT THE N-TERMINUS MET166 AND GLU221 REPLACED AGAINST CYS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN

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Sample preparation

Sample conditionsIonic strength: 0.01 M / pH: 4.5 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
OPALpKORADI, BILLETER, GUNTERTrefinement
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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