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Yorodumi- PDB-6jpd: Mouse receptor-interacting protein kinase 3 (RIP3) amyloid struct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jpd | ||||||
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Title | Mouse receptor-interacting protein kinase 3 (RIP3) amyloid structure by solid-state NMR | ||||||
Components | Receptor-interacting serine/threonine-protein kinase 3 | ||||||
Keywords | PROTEIN FIBRIL / programmed necrosis / amyloid | ||||||
Function / homology | Function and homology information RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of activated T cell proliferation / Regulation of necroptotic cell death ...RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of activated T cell proliferation / Regulation of necroptotic cell death / regulation of type II interferon production / programmed necrotic cell death / necroptotic signaling pathway / TRP channels / positive regulation of necroptotic process / regulation of reactive oxygen species metabolic process / activation of protein kinase activity / T cell homeostasis / non-canonical NF-kappaB signal transduction / necroptotic process / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / reactive oxygen species metabolic process / thymus development / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / T cell differentiation in thymus / regulation of apoptotic process / defense response to virus / amyloid fibril formation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein-containing complex binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLID-STATE NMR / simulated annealing | ||||||
Authors | Wu, X.L. / Hu, H. / Zhang, J. / Dong, X.Q. / Wang, J. / Schwieters, C. / Wang, H.Y. / Lu, J.X. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: The amyloid structure of mouse RIPK3 (receptor interacting protein kinase 3) in cell necroptosis. Authors: Wu, X.L. / Hu, H. / Dong, X.Q. / Zhang, J. / Wang, J. / Schwieters, C.D. / Liu, J. / Wu, G.X. / Li, B. / Lin, J.Y. / Wang, H.Y. / Lu, J.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jpd.cif.gz | 323 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jpd.ent.gz | 256 KB | Display | PDB format |
PDBx/mmJSON format | 6jpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/6jpd ftp://data.pdbj.org/pub/pdb/validation_reports/jp/6jpd | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9454.359 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk3, Rip3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9QZL0, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0 mM / Label: H2O / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: medoid | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |