+Open data
-Basic information
Entry | Database: PDB / ID: 4zzh | ||||||
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Title | SIRT1/Activator Complex | ||||||
Components | NAD-dependent protein deacetylase sirtuin-1 | ||||||
Keywords | Hydrolase/hydrolase activator / Sirtuin / Activator / Deacylase / Complex / Hydrolase-hydrolase activator complex | ||||||
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 / leptin-mediated signaling pathway / NAD-dependent histone H3K9 deacetylase activity / positive regulation of smooth muscle cell differentiation / NAD-dependent histone H4K16 deacetylase activity / negative regulation of peptidyl-lysine acetylation / regulation of brown fat cell differentiation / deacetylase activity / response to leptin / bHLH transcription factor binding / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / intracellular triglyceride homeostasis / : / peptidyl-lysine acetylation / positive regulation of adaptive immune response / negative regulation of androgen receptor signaling pathway / regulation of centrosome duplication / rDNA heterochromatin / ovulation from ovarian follicle / single strand break repair / negative regulation of cAMP-dependent protein kinase activity / regulation of bile acid biosynthetic process / DNA methylation-dependent heterochromatin formation / NAD-dependent protein lysine deacetylase activity / rDNA heterochromatin formation / negative regulation of phosphorylation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / negative regulation of protein acetylation / chromatin silencing complex / negative regulation of TOR signaling / protein deacetylation / UV-damage excision repair / positive regulation of MHC class II biosynthetic process / protein lysine deacetylase activity / negative regulation of helicase activity / positive regulation of cAMP-dependent protein kinase activity / DNA repair-dependent chromatin remodeling / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / positive regulation of double-strand break repair / muscle organ development / Regulation of FOXO transcriptional activity by acetylation / nuclear inner membrane / histone deacetylase activity / stress-induced premature senescence / negative regulation of fat cell differentiation / 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 NF-kappaB transcription factor activity / intracellular glucose homeostasis / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of cellular senescence / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of macroautophagy / macrophage differentiation / positive regulation of cholesterol efflux / white fat cell differentiation / negative regulation of cell cycle / regulation of glucose metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / NAD+ binding / Regulation of HSF1-mediated heat shock response / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / fatty acid homeostasis / positive regulation of blood vessel endothelial cell migration / cellular response to glucose starvation / heterochromatin / heterochromatin formation / energy homeostasis / regulation of cellular response to heat / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / positive regulation of gluconeogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of DNA repair Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1001 Å | ||||||
Authors | Dai, H. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Crystallographic structure of a small molecule SIRT1 activator-enzyme complex. Authors: Dai, H. / Case, A.W. / Riera, T.V. / Considine, T. / Lee, J.E. / Hamuro, Y. / Zhao, H. / Jiang, Y. / Sweitzer, S.M. / Pietrak, B. / Schwartz, B. / Blum, C.A. / Disch, J.S. / Caldwell, R. / ...Authors: Dai, H. / Case, A.W. / Riera, T.V. / Considine, T. / Lee, J.E. / Hamuro, Y. / Zhao, H. / Jiang, Y. / Sweitzer, S.M. / Pietrak, B. / Schwartz, B. / Blum, C.A. / Disch, J.S. / Caldwell, R. / Szczepankiewicz, B. / Oalmann, C. / Yee Ng, P. / White, B.H. / Casaubon, R. / Narayan, R. / Koppetsch, K. / Bourbonais, F. / Wu, B. / Wang, J. / Qian, D. / Jiang, F. / Mao, C. / Wang, M. / Hu, E. / Wu, J.C. / Perni, R.B. / Vlasuk, G.P. / Ellis, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zzh.cif.gz | 154.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zzh.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/4zzh ftp://data.pdbj.org/pub/pdb/validation_reports/zz/4zzh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40125.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT1, SIR2L1 / Production host: Escherichia coli (E. coli) References: UniProt: Q96EB6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-4TO / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium chloride, 0.1 M Tris pH 8.5, and 16 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→45.67 Å / Num. obs: 13615 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 3.1→3.34 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Resolution: 3.1001→45.666 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1001→45.666 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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