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Yorodumi- PDB-4y6o: Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y6o | ||||||
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Title | Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr) | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / sirtuin / SIRT / NAD-dependent deacetylase / myristoylated lysine / HYDROLASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / cellular lipid catabolic process / negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / negative regulation of striated muscle tissue development / positive regulation of translational initiation by iron / : / response to macrophage colony-stimulating factor / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / response to 3,3',5-triiodo-L-thyronine / positive regulation of meiotic nuclear division / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / NAD-dependent histone H4K16 deacetylase activity / : / positive regulation of attachment of spindle microtubules to kinetochore / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / response to gold nanoparticle / tubulin deacetylation / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / negative regulation of myelination / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / response to isolation stress / death receptor agonist activity / cellular response to toxic substance / inflammatory response to wounding / lateral loop / NLRP3 inflammasome complex assembly / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of I-kappaB phosphorylation / TNF signaling / peptidyl-lysine deacetylation / sequestering of triglyceride / positive regulation of action potential / positive regulation of protein transport / mitotic nuclear membrane reassembly / positive regulation of interleukin-18 production / negative regulation of NLRP3 inflammasome complex assembly / epithelial cell proliferation involved in salivary gland morphogenesis / tubulin deacetylase activity / toll-like receptor 3 signaling pathway / leukocyte migration involved in inflammatory response / embryonic digestive tract development / positive regulation of superoxide dismutase activity / necroptotic signaling pathway / paranode region of axon / Schmidt-Lanterman incisure / regulation of exit from mitosis / vascular endothelial growth factor production / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of neuroinflammatory response / response to fructose / leukocyte tethering or rolling / myelination in peripheral nervous system / positive regulation of fatty acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / rDNA heterochromatin formation / positive regulation of synoviocyte proliferation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / positive regulation of mononuclear cell migration / positive regulation of fever generation / chromatin silencing complex / regulation of phosphorylation / negative regulation of myoblast differentiation / positive regulation of protein localization to cell surface / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / TNFR1-mediated ceramide production / juxtaparanode region of axon / macrophage activation involved in immune response / negative regulation of glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / positive regulation of oocyte maturation / positive regulation of membrane protein ectodomain proteolysis / negative regulation of oxidative phosphorylation / negative regulation of systemic arterial blood pressure / positive regulation of cytokine production involved in inflammatory response / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kudo, N. / Ito, A. / Yoshida, M. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation. Authors: Feldman, J.L. / Dittenhafer-Reed, K.E. / Kudo, N. / Thelen, J.N. / Ito, A. / Yoshida, M. / Denu, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y6o.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y6o.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 4y6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/4y6o ftp://data.pdbj.org/pub/pdb/validation_reports/y6/4y6o | HTTPS FTP |
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-Related structure data
Related structure data | 4y6lC 4y6qC 1j8fS 3zgoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33201.223 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 52-291, 304-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Plasmid: pGEX-4T3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8IXJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Protein/peptide | Mass: 911.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01375*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 77514 / % possible obs: 95.7 % / Redundancy: 1.9 % / Rsym value: 0.049 / Net I/σ(I): 14.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J8F, 3ZGO Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.827 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.931 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→20 Å
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