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Yorodumi- PDB-2kkg: NMR structure of the octarepeat region of prion protein bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kkg | ||||||
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Title | NMR structure of the octarepeat region of prion protein bound to pentosan polysulfate | ||||||
Components | Major prion protein | ||||||
Keywords | MEMBRANE PROTEIN / prion protein / octapeptide repeats / pentosan polysulfate / sulfated glycans / Cell membrane / Disulfide bond / Glycoprotein / Golgi apparatus / GPI-anchor / Lipoprotein / Membrane / Prion | ||||||
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 / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade ...regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / cuprous ion binding / negative regulation of amyloid-beta formation / 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 / protein sequestering activity / negative regulation of protein phosphorylation / molecular condensate scaffold activity / 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 peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / amyloid fibril formation / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / cell cycle / 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 | Mesocricetus auratus (golden hamster) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
Model details | closest to the average, model 2 | ||||||
Authors | Taubner, L.M. / Caughey, B. / Copie, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structure of the flexible amino-terminal domain of prion protein bound to a sulfated glycan. Authors: Taubner, L.M. / Bienkiewicz, E.A. / Copie, V. / Caughey, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kkg.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kkg.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 2kkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/2kkg ftp://data.pdbj.org/pub/pdb/validation_reports/kk/2kkg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8696.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Gene: PRNP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04273 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: residues 57-91 of Syrian hamster prion protein | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 5.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 | |||||||||||||||||||||
NMR constraints | NOE constraints total: 285 / NOE intraresidue total count: 81 / NOE medium range total count: 59 / NOE sequential total count: 145 | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.2 Å | |||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.99 Å |