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Yorodumi- PDB-8ez6: The DBC1/SIRT1 Interaction is Choreographed by Post-translational... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ez6 | ||||||
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Title | The DBC1/SIRT1 Interaction is Choreographed by Post-translational Modification | ||||||
Components | Cell cycle and apoptosis regulator protein 2 | ||||||
Keywords | GENE REGULATION / DBC1 / S1-like / insulin signaling / liver metabolism / chaperone | ||||||
Function / homology | Function and homology information DBIRD complex / regulation of protein deacetylation / positive regulation of DNA damage checkpoint / adenyl-nucleotide exchange factor activity / mitochondrial fragmentation involved in apoptotic process / negative regulation of catalytic activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cell cycle / enzyme inhibitor activity / RNA polymerase II complex binding ...DBIRD complex / regulation of protein deacetylation / positive regulation of DNA damage checkpoint / adenyl-nucleotide exchange factor activity / mitochondrial fragmentation involved in apoptotic process / negative regulation of catalytic activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cell cycle / enzyme inhibitor activity / RNA polymerase II complex binding / Regulation of HSF1-mediated heat shock response / response to UV / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA splicing / regulation of DNA-templated transcription elongation / regulation of protein stability / regulation of circadian rhythm / negative regulation of cell growth / Wnt signaling pathway / spindle / mRNA processing / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / rhythmic process / mitochondrial matrix / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / DNA damage response / chromatin / enzyme binding / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Krzysiak, T.C. / Gronenborn, A.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2024 Title: Inhibitory protein-protein interactions of the SIRT1 deacetylase are choreographed by post-translational modification. Authors: Krzysiak, T.C. / Choi, Y.J. / Kim, Y.J. / Yang, Y. / DeHaven, C. / Thompson, L. / Ponticelli, R. / Mermigos, M.M. / Thomas, L. / Marquez, A. / Sipula, I. / Kemper, J.K. / Jurczak, M. / ...Authors: Krzysiak, T.C. / Choi, Y.J. / Kim, Y.J. / Yang, Y. / DeHaven, C. / Thompson, L. / Ponticelli, R. / Mermigos, M.M. / Thomas, L. / Marquez, A. / Sipula, I. / Kemper, J.K. / Jurczak, M. / Thomas, G. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ez6.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ez6.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 8ez6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ez6_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 8ez6_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 8ez6_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 8ez6_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/8ez6 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/8ez6 | HTTPS FTP |
-Related structure data
Related structure data | 1wfqS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8000.075 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCAR2, DBC1, KIAA1967 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N163 #2: 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: 1.84 Å3/Da / Density % sol: 33.25 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / Details: 0.1M sodium acetate pH 4.6, 2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.32 Å / Num. obs: 8285 / % possible obs: 97.9 % / Redundancy: 13.59 % / Biso Wilson estimate: 20.73 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 37.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 13.69 % / Rmerge(I) obs: 0.127 / Num. unique obs: 602 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WFQ Resolution: 2→39.32 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 22.3753 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: 24.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.32 Å
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Refine LS restraints |
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LS refinement shell |
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