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- PDB-1qm3: Human prion protein fragment 121-230 -

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Basic information

Entry
Database: PDB / ID: 1qm3
TitleHuman prion protein fragment 121-230
ComponentsPRION PROTEIN
KeywordsPRION PROTEIN / PRION / BRAIN / GLYCOPROTEIN / GPI-ANCHOR / POLYMORPHISM / DISEASE MUTATION
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
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. / Liu, A. / Luhrs, T. / Wuthrich, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: NMR Solution Structure of the Human Prion Protein
Authors: Zahn, R. / Liu, A. / Luhrs, T. / Riek, R. / Von Schroetter, C. / Garcia, F.L. / Billeter, M. / Calzolai, L. / Wider, G. / Wuthrich, K.
History
DepositionSep 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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: PRION PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,1611
Polymers13,1611
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 #12

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Components

#1: Protein PRION PROTEIN / PRP / MAJOR PRION PROTEIN / PRP27-30 / PRP33-35C / (ASCR).PRP


Mass: 13160.596 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) / Cellular location: EXTRACELLULAR / Gene: PRNP / Organ: BRAIN / Plasmid: PRSET A / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04156
Sequence details2 RESIDUES (GLY SER) INSERTED AT THE N-TERMINUS

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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

DetailsContents: 90% WATER / 10% D2O
Sample conditionsIonic strength: 0.01 / 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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