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Yorodumi- PDB-2k1d: NMR Studies of a Pathogenic Mutant (D178N) of the Human Prion Protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k1d | ||||||
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Title | NMR Studies of a Pathogenic Mutant (D178N) of the Human Prion Protein | ||||||
Components | Major prion protein | ||||||
Keywords | UNKNOWN FUNCTION / prion protein / M/V 129 polymorphism / D178N / disease mutation / FFI / GSS / Glycoprotein / Golgi apparatus / GPI-anchor / Lipoprotein / Membrane | ||||||
Function / homology | Function and homology information : / 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 / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport ...: / 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 / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of interleukin-2 production / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / negative regulation of amyloid-beta formation / cuprous ion binding / negative regulation of activated T cell proliferation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / negative regulation of type II interferon production / : / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / positive regulation of protein tyrosine kinase activity / response to cadmium ion / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / neuron projection maintenance / molecular condensate scaffold activity / tubulin binding / protein sequestering activity / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / postsynapse / nuclear membrane / response to oxidative stress / protease binding / transmembrane transporter binding / postsynaptic density / learning or memory / molecular adaptor activity / regulation of cell cycle / cell cycle / copper ion binding / membrane raft / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, TORSION ANGLE DYNAMICS | ||||||
Authors | Mills, J.L. / Surewicz, K. / Surewicz, W.K. / Sonnichsen, F.D. | ||||||
Citation | Journal: To be Published Title: Residue 129 polymorphism and conformational dynamics of familial prion diseases associated with the human prion protein variant D178N Authors: Mills, J.L. / Surewicz, K. / Surewicz, W.K. / Sonnichsen, F.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k1d.cif.gz | 672.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k1d.ent.gz | 568.4 KB | Display | PDB format |
PDBx/mmJSON format | 2k1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/2k1d ftp://data.pdbj.org/pub/pdb/validation_reports/k1/2k1d | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16492.281 Da / Num. of mol.: 1 / Fragment: UNP residue 90-231 / Mutation: D178N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRNP, PRIP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04156 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING STANDARD TRIPLE RESONANCE EXPERIMENTS RECORDED WITH 13C, 15N LABELED PROTEIN |
-Sample preparation
Details | Contents: 350 uM [U-99% 13C; U-99% 15N] V129/D178N prion protein, 10 mM sodium acetate, 100 uM sodium azide, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 20 / pH: 4.6 / Pressure: AMBIENT / Temperature: 299 K |
-NMR measurement
NMR spectrometer | Type: BRUKER AVANCE600 / Manufacturer: Bruker / Model: AVANCE600 / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, TORSION ANGLE DYNAMICS / Software ordinal: 1 | ||||||||||||||||
NMR constraints | NOE constraints total: 819 / NOE intraresidue total count: 306 / NOE long range total count: 123 / NOE medium range total count: 117 / NOE sequential total count: 273 | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |