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Yorodumi- PDB-4ig9: Structure of NAD-dependent protein deacetylase sirtuin-1 (open st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ig9 | ||||||
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Title | Structure of NAD-dependent protein deacetylase sirtuin-1 (open state, 2.64 A) | ||||||
Components | (NAD-dependent protein deacetylase sirtuin-1) x 2 | ||||||
Keywords | HYDROLASE / deacetylase | ||||||
Function / homology | Function and homology information negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / eNoSc complex / histone H4K12 deacetylase activity / histone H3K deacetylase activity / NAD-dependent histone decrotonylase activity / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / protein depropionylation ...negative regulation of prostaglandin biosynthetic process / regulation of smooth muscle cell apoptotic process / maintenance of nucleus location / eNoSc complex / histone H4K12 deacetylase activity / histone H3K deacetylase activity / NAD-dependent histone decrotonylase activity / negative regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of cellular response to testosterone stimulus / protein depropionylation / protein-propionyllysine depropionylase activity / regulation of peroxisome proliferator activated receptor signaling pathway / regulation of transcription by glucose / regulation of protein serine/threonine kinase activity / positive regulation of macrophage apoptotic process / NAD-dependent histone H3K14 deacetylase activity / negative regulation of triglyceride biosynthetic process / regulation of endodeoxyribonuclease activity / triglyceride mobilization / behavioral response to starvation / pyrimidine dimer repair by nucleotide-excision repair / keratin filament binding / HLH domain binding / regulation of lipid storage / Regulation of MITF-M dependent genes involved in metabolism / NAD-dependent histone H3K9 deacetylase activity / leptin-mediated signaling pathway / negative regulation of peptidyl-lysine acetylation / NAD-dependent histone H4K16 deacetylase activity / deacetylase activity / regulation of brown fat cell differentiation / positive regulation of smooth muscle cell differentiation / bHLH transcription factor binding / response to leptin / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / intracellular triglyceride homeostasis / peptidyl-lysine acetylation / negative regulation of androgen receptor signaling pathway / positive regulation of adaptive immune response / regulation of centrosome duplication / rDNA heterochromatin / ovulation from ovarian follicle / negative regulation of cAMP-dependent protein kinase activity / single strand break repair / regulation of bile acid biosynthetic process / NAD-dependent protein lysine deacetylase activity / negative regulation of signal transduction by p53 class mediator / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / negative regulation of protein acetylation / negative regulation of phosphorylation / chromatin silencing complex / NAD-dependent histone deacetylase activity / protein deacetylation / positive regulation of MHC class II biosynthetic process / UV-damage excision repair / DNA methylation-dependent heterochromatin formation / protein lysine deacetylase activity / negative regulation of TOR signaling / positive regulation of cAMP-dependent protein kinase activity / negative regulation of helicase activity / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / Regulation of FOXO transcriptional activity by acetylation / nuclear inner membrane / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair / white fat cell differentiation / muscle organ development / stress-induced premature senescence / positive regulation of cholesterol efflux / negative regulation of NF-kappaB transcription factor activity / histone deacetylase activity / DNA synthesis involved in DNA repair / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of fat cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / intracellular glucose homeostasis / regulation of mitotic cell cycle / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / macrophage differentiation / positive regulation of macroautophagy / negative regulation of cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of glucose metabolic process / NAD+ binding / Regulation of HSF1-mediated heat shock response / positive regulation of blood vessel endothelial cell migration / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA repair / fatty acid homeostasis / positive regulation of adipose tissue development / heterochromatin / cellular response to glucose starvation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of cellular response to heat / positive regulation of insulin receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / energy homeostasis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å | ||||||
Authors | Davenport, A.M. / Huber, F.M. / Hoelz, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structural and Functional Analysis of Human SIRT1. Authors: Davenport, A.M. / Huber, F.M. / Hoelz, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ig9.cif.gz | 240.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ig9.ent.gz | 196 KB | Display | PDB format |
PDBx/mmJSON format | 4ig9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ig9_validation.pdf.gz | 489.5 KB | Display | wwPDB validaton report |
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Full document | 4ig9_full_validation.pdf.gz | 500.9 KB | Display | |
Data in XML | 4ig9_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 4ig9_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/4ig9 ftp://data.pdbj.org/pub/pdb/validation_reports/ig/4ig9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 31833.107 Da / Num. of mol.: 4 / Fragment: UNP residues 234-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L1, SIRT1 / Production host: Escherichia coli (E. coli) References: UniProt: Q96EB6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Protein/peptide | Mass: 3544.836 Da / Num. of mol.: 4 / Fragment: UNP residues 641-665 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L1, SIRT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EB6 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.36 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 20 mM TRIS-HCl, 10 % PEG 20,000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2676 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2676 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→20 Å / Num. obs: 68583 / % possible obs: 97.1 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.64→19.941 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 30.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1737 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→19.941 Å
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Refine LS restraints |
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LS refinement shell |
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