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- PDB-6uyo: Crystal structure of K37-acetylated SUMO1 in complex with PML-SIM -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uyo | |||||||||
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Title | Crystal structure of K37-acetylated SUMO1 in complex with PML-SIM | |||||||||
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![]() | NUCLEAR PROTEIN/PROTEIN BINDING / SUMO1 / PML / SUMO INTERACTION MOTIF / NUCLEAR PROTEIN-PROTEIN BINDING complex | |||||||||
Function / homology | ![]() regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase activity / SUMO-modified protein reader activity / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / protein localization to nuclear pore / suppression of viral release by host / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins ...regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase activity / SUMO-modified protein reader activity / positive regulation of protein localization to chromosome, telomeric region / positive regulation of peptidyl-lysine acetylation / protein localization to nuclear pore / suppression of viral release by host / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / SUMO binding / septin ring / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / negative regulation of telomerase activity / regulation of calcium ion transmembrane transport / regulation of double-strand break repair / SUMOylation of DNA methylation proteins / myeloid cell differentiation / positive regulation of telomere maintenance / SMAD protein signal transduction / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / maintenance of protein location in nucleus / protein-containing complex localization / Maturation of nucleoprotein / endoplasmic reticulum calcium ion homeostasis / Transferases; Acyltransferases; Aminoacyltransferases / positive regulation of extrinsic apoptotic signaling pathway / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / SUMO transferase activity / branching involved in mammary gland duct morphogenesis / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of interleukin-1 beta production / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of protein import into nucleus / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / cobalt ion binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SMAD binding / entrainment of circadian clock by photoperiod / protein monoubiquitination / positive regulation of signal transduction by p53 class mediator / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / protein sumoylation / negative regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / potassium channel regulator activity / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / cell fate commitment / protein targeting / cellular response to interleukin-4 / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / response to UV / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / Regulation of TP53 Activity through Acetylation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to cadmium ion / negative regulation of ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / SUMOylation of chromatin organization proteins / negative regulation of angiogenesis / transforming growth factor beta receptor signaling pathway / SUMOylation of transcription cofactors / cellular response to leukemia inhibitory factor / response to cytokine / response to gamma radiation / circadian regulation of gene expression / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / regulation of circadian rhythm / negative regulation of DNA-binding transcription factor activity / negative regulation of cell growth / PML body Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wahba, H.M. / Gagnon, C. / Mascle, X.H. / Lussier-Price, M. / Sakaguchi, K. / Omichinski, J.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Acetylation of SUMO1 Alters Interactions with the SIMs of PML and Daxx in a Protein-Specific Manner. Authors: Mascle, X.H. / Gagnon, C. / Wahba, H.M. / Lussier-Price, M. / Cappadocia, L. / Sakaguchi, K. / Omichinski, J.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.6 KB | Display | ![]() |
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PDB format | ![]() | 93.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 448.8 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uypC ![]() 6uyqC ![]() 6uyrC ![]() 6uysC ![]() 6uytC ![]() 6uyuC ![]() 6uyvC ![]() 6uyxC ![]() 6uyyC ![]() 6uyzC ![]() 4wjoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 9567.801 Da / Num. of mol.: 2 / Mutation: C52A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2976.985 Da / Num. of mol.: 2 / Mutation: E574Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.639→37.238 Å / Num. obs: 25537 / % possible obs: 94.78 % / Redundancy: 4.4 % / CC1/2: 0.999 / Net I/σ(I): 12.21 |
Reflection shell | Resolution: 1.639→1.698 Å / Redundancy: 2.9 % / Num. unique obs: 1618 / CC1/2: 0.62 / % possible all: 60.17 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WJO Resolution: 1.639→37.238 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147 Å2 / Biso mean: 40.2452 Å2 / Biso min: 20.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.639→37.238 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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