+Open data
-Basic information
Entry | Database: PDB / ID: 2joh | ||||||
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Title | NMR structure of rabbit prion protein mutation S173N | ||||||
Components | Major prion protein | ||||||
Keywords | UNKNOWN FUNCTION / prion protein | ||||||
Function / homology | Function and homology information 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 / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of interleukin-2 production ...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 / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of interleukin-2 production / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of amyloid-beta formation / cuprous ion binding / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / : / positive regulation of protein targeting to membrane / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / molecular condensate scaffold activity / protein sequestering activity / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / 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 / microtubule binding / nuclear membrane / response to oxidative stress / protease binding / learning or memory / copper ion binding / membrane raft / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Li, J. / Lin, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Unique structural characteristics of the rabbit prion protein. Authors: Wen, Y. / Li, J. / Yao, W. / Xiong, M. / Hong, J. / Peng, Y. / Xiao, G. / Lin, D. #1: Journal: J.Biomol.Nmr / Year: 2007 Title: 1H, 13C and 15N resonance assignments of rabbit prion protein (91-228). Authors: Li, J. / Mei, F.H. / Xiao, G.F. / Guo, C.Y. / Lin, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2joh.cif.gz | 553.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2joh.ent.gz | 463.5 KB | Display | PDB format |
PDBx/mmJSON format | 2joh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/2joh ftp://data.pdbj.org/pub/pdb/validation_reports/jo/2joh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 17024.965 Da / Num. of mol.: 1 / Fragment: residues 91-228 / Mutation: S173N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PRNP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: Q95211 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8 mM protein, 20 mM sodium acetate, 100% D2O / Solvent system: 100% D2O |
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Sample | Conc.: 20 mM / Component: sodium acetate |
Sample conditions | pH: 4.5 / Pressure: ambient / Temperature: 298.13 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 15 |