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Yorodumi- PDB-2lv1: Solution-state NMR structure of prion protein mutant V210I at neu... -
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-Basic information
Entry | Database: PDB / ID: 2lv1 | ||||||
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Title | Solution-state NMR structure of prion protein mutant V210I at neutral pH | ||||||
Components | Major prion protein | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
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 / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / 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 / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / 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 / tubulin binding / 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 / negative regulation of DNA-binding transcription factor activity / 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 / protein-folding chaperone binding / postsynapse / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / transmembrane transporter binding / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / cell cycle / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics, simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Biljan, I. / Ilc, G. / Giachin, G. / Legname, G. / Plavec, J. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structural Rearrangements at Physiological pH: Nuclear Magnetic Resonance Insights from the V210I Human Prion Protein Mutant. Authors: Biljan, I. / Ilc, G. / Giachin, G. / Plavec, J. / Legname, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lv1.cif.gz | 884.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lv1.ent.gz | 754 KB | Display | PDB format |
PDBx/mmJSON format | 2lv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lv1_validation.pdf.gz | 548.5 KB | Display | wwPDB validaton report |
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Full document | 2lv1_full_validation.pdf.gz | 846.9 KB | Display | |
Data in XML | 2lv1_validation.xml.gz | 59.1 KB | Display | |
Data in CIF | 2lv1_validation.cif.gz | 95.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/2lv1 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/2lv1 | HTTPS FTP |
-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: 16654.555 Da / Num. of mol.: 1 / Fragment: UNP residues 90-231 / Mutation: V210I 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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-Sample preparation
Details | Contents: 0.6 mM [U-100% 13C; U-100% 15N] prion protein mutation V210I, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.6 mM / Component: prion protein mutation V210I-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 20 mM / pH: 7.2 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics, simulated annealing / Software ordinal: 1 Details: THE FINAL STEP OF STRUCTURE REFINEMENT WAS PERFORMED IN EXPLICIT WATER-BOX, USED FOR AUTOMATED NMR PROTEIN STRUCTURE CALCULATION | ||||||||||||||||||||
NMR constraints | NOE constraints total: 1929 / NOE intraresidue total count: 452 / NOE long range total count: 481 / NOE medium range total count: 516 / NOE sequential total count: 480 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 79 / Protein psi angle constraints total count: 79 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.7 ° / Maximum upper distance constraint violation: 0.189 Å / Torsion angle constraint violation method: Talos + |