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Open data
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Basic information
Entry | Database: PDB / ID: 8dji | ||||||
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Title | Ternary complex of SUMO1 with the SIM of PML and zinc | ||||||
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![]() | NUCLEAR PROTEIN / SUMO1 / PML Nuclear Bodies / Zinc / auto-inhibition / Daxx | ||||||
Function / homology | ![]() regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / negative regulation of potassium ion transmembrane transporter activity / suppression of viral release by host / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / negative regulation of delayed rectifier potassium channel activity ...regulation of calcium ion transport into cytosol / ubiquitin-like protein ligase activity / negative regulation of translation in response to oxidative stress / positive regulation of protein localization to chromosome, telomeric region / negative regulation of potassium ion transmembrane transporter activity / suppression of viral release by host / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / negative regulation of delayed rectifier potassium channel activity / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / SUMO binding / small protein activating enzyme binding / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / SMAD protein signal transduction / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / myeloid cell differentiation / XY body / SUMOylation of SUMOylation proteins / protein-containing complex localization / maintenance of protein location in nucleus / regulation of calcium ion transmembrane transport / regulation of double-strand break repair / endoplasmic reticulum calcium ion homeostasis / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / branching involved in mammary gland duct morphogenesis / oncogene-induced cell senescence / Regulation of RUNX1 Expression and Activity / negative regulation of mitotic cell cycle / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / positive regulation of extrinsic apoptotic signaling pathway / Postmitotic nuclear pore complex (NPC) reformation / cobalt ion binding / Maturation of nucleoprotein / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of interleukin-1 beta production / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / entrainment of circadian clock by photoperiod / SMAD binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / cellular response to cadmium ion / ubiquitin-like protein ligase binding / roof of mouth development / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of signal transduction by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / cell fate commitment / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / postsynaptic cytosol / potassium channel regulator activity / transporter activator activity / Regulation of IFNG signaling / nuclear pore / protein targeting / negative regulation of DNA-binding transcription factor activity / regulation of cell adhesion / SUMOylation of DNA damage response and repair proteins / response to UV / retinoic acid receptor signaling pathway / presynaptic cytosol / Regulation of PTEN localization / Regulation of TP53 Activity through Acetylation / extrinsic apoptotic signaling pathway / positive regulation of defense response to virus by host / response to cytokine / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to interleukin-4 / transforming growth factor beta receptor signaling pathway / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / negative regulation of angiogenesis / cellular response to leukemia inhibitory factor / response to gamma radiation / DNA damage response, signal transduction by p53 class mediator / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / circadian regulation of gene expression / Formation of Incision Complex in GG-NER / protein tag activity / regulation of circadian rhythm / negative regulation of cell growth Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lussier-Price, M. / Wahba, H.M. / Mascle, X.H. / Cappadocia, L. / Bourdeau, V. / Gagnon, C. / Igelmann, S. / Sakaguchi, K. / Ferbeyre, G. / Omichinski, J.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1. Authors: Lussier-Price, M. / Wahba, H.M. / Mascle, X.H. / Cappadocia, L. / Bourdeau, V. / Gagnon, C. / Igelmann, S. / Sakaguchi, K. / Ferbeyre, G. / 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 | ![]() | 69.6 KB | Display | ![]() |
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PDB format | ![]() | 50.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8djhC ![]() 6v7pS 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
#1: Protein | Mass: 11043.335 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 2976.985 Da / Num. of mol.: 1 / Fragment: SIM Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P29590, Transferases; Acyltransferases; Aminoacyltransferases | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100 mM HEPES pH 7.0, 19 to 31 % (w/v) PEG 3350, and 1-5 mM zinc chloride |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→32 Å / Num. obs: 14192 / % possible obs: 96.58 % / Redundancy: 5.5 % / CC1/2: 0.982 / Net I/σ(I): 5.34 |
Reflection shell | Resolution: 1.97→2.044 Å / Num. unique obs: 637 / CC1/2: 0.263 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6V7P Resolution: 1.97→32 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30 / 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 max: 70.06 Å2 / Biso mean: 34.7233 Å2 / Biso min: 16.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→32 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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