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- PDB-8ccw: Crystal structure of human Sirt3 in complex with an acetylated HI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ccw | ||||||
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Title | Crystal structure of human Sirt3 in complex with an acetylated HIV1 Tat-46-54 substrate peptide | ||||||
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![]() | SIGNALING PROTEIN / Sirtuin / substrate / HIV / Tat / complex | ||||||
Function / homology | ![]() viral gene expression / trans-activation response element binding / positive regulation of catalase activity / regulatory region RNA binding / positive regulation of ceramide biosynthetic process / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / peptidyl-lysine deacetylation / symbiont-mediated suppression of host translation initiation ...viral gene expression / trans-activation response element binding / positive regulation of catalase activity / regulatory region RNA binding / positive regulation of ceramide biosynthetic process / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / peptidyl-lysine deacetylation / symbiont-mediated suppression of host translation initiation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / host cell nucleolus / protein deacetylation / NAD-dependent histone deacetylase activity / actinin binding / Regulation of FOXO transcriptional activity by acetylation / negative regulation of peptidyl-threonine phosphorylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / RNA-binding transcription regulator activity / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / transferase activity / sequence-specific DNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / mitochondrial matrix / protein domain specific binding / virus-mediated perturbation of host defense response / DNA-templated transcription / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / extracellular region / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Adolph, R.S. / Steegborn, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular Mechanism of Sirtuin 1 Inhibition by Human Immunodeficiency Virus 1 Tat Protein. Authors: Adolph, R.S. / Beck, E. / Schweimer, K. / Di Fonzo, A. / Weyand, M. / Rosch, P. / Wohrl, B.M. / Steegborn, C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.7 KB | Display | ![]() |
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PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.9 KB | Display | ![]() |
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Full document | ![]() | 439.5 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cczC ![]() 4fvtS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31340.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NTG7, protein acetyllysine N-acetyltransferase |
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#2: Protein/peptide | Mass: 1224.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: acetylated at K50 / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM ac-Tat-46-54 for 60 min at 293.15 K. The complex was crystallized ...Details: 10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM ac-Tat-46-54 for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM MES, pH 6.0, 30% (w/v) PEG 200, 5% (w/v) PEG 3000 as reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2018 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→39.36 Å / Num. obs: 47332 / % possible obs: 99.89 % / Redundancy: 11.2 % / Biso Wilson estimate: 31.51 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 13.93 |
Reflection shell | Resolution: 1.65→1.709 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 4698 / CC1/2: 0.469 / CC star: 0.799 / % possible all: 99.94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FVT Resolution: 1.65→39.36 Å / SU ML: 0.2872 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9404 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 36.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.36 Å
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Refine LS restraints |
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LS refinement shell |
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