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Yorodumi- PDB-6uyq: Crystal structure of K45-acetylated SUMO1 in complex with PML-SIM -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uyq | |||||||||
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Title | Crystal structure of K45-acetylated SUMO1 in complex with PML-SIM | |||||||||
Components |
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Keywords | NUCLEAR PROTEIN/PROTEIN BINDING / SUMO1 / PML / SUMO INTERACTION MOTIF / PHOSPHOSIM / NUCLEAR PROTEIN-PROTEIN BINDING complex | |||||||||
Function / homology | Function and homology information regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase 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 ...regulation of calcium ion transport into cytosol / negative regulation of translation in response to oxidative stress / ubiquitin-like protein ligase 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 / fibroblast migration / positive regulation of apoptotic process involved in mammary gland involution / : / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / myeloid cell differentiation / positive regulation of telomere maintenance / SMAD protein signal transduction / regulation of double-strand break repair / 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 / positive regulation of extrinsic apoptotic signaling pathway / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Transferases; Acyltransferases; Aminoacyltransferases / oncogene-induced cell senescence / SUMO transferase activity / Regulation of RUNX1 Expression and Activity / branching involved in mammary gland duct morphogenesis / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of mitotic cell cycle / Maturation of nucleoprotein / negative regulation of interleukin-1 beta production / SUMOylation of chromatin organization proteins / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of protein import into nucleus / cobalt ion binding / retinoic acid receptor signaling pathway / cell fate commitment / SUMOylation of ubiquitinylation proteins / roof of mouth development / ubiquitin-specific protease binding / entrainment of circadian clock by photoperiod / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SMAD binding / transcription factor binding / positive regulation of signal transduction by p53 class mediator / negative regulation of telomere maintenance via telomerase / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to cadmium ion / potassium channel regulator activity / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein targeting / cellular response to interleukin-4 / regulation of cell adhesion / negative regulation of ubiquitin-dependent protein catabolic process / SUMOylation of DNA damage response and repair proteins / nuclear pore / negative regulation of angiogenesis / Regulation of IFNG signaling / 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 / Regulation of PTEN localization / transforming growth factor beta receptor signaling pathway / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / response to cytokine / cellular response to leukemia inhibitory factor / regulation of circadian rhythm / response to gamma radiation / Transcriptional regulation of granulopoiesis / HCMV Early Events / circadian regulation of gene expression / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / cellular senescence / negative regulation of cell growth Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å | |||||||||
Authors | Wahba, H.M. / Gagnon, C. / Mascle, X.H. / Lussier-Price, M. / Cappadocia, L. / Sakaguchi, K. / Omichinski, J.G. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Structure / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uyq.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uyq.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 6uyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uyq_validation.pdf.gz | 416.4 KB | Display | wwPDB validaton report |
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Full document | 6uyq_full_validation.pdf.gz | 416.4 KB | Display | |
Data in XML | 6uyq_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6uyq_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/6uyq ftp://data.pdbj.org/pub/pdb/validation_reports/uy/6uyq | HTTPS FTP |
-Related structure data
Related structure data | 6uyoC 6uypC 6uyrC 6uysC 6uytC 6uyuC 6uyvC 6uyxC 6uyyC 6uyzC 4wjoS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 9567.801 Da / Num. of mol.: 1 / Mutation: C52A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Plasmid: PGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: P63165 |
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#2: Protein/peptide | Mass: 2976.985 Da / Num. of mol.: 1 / Mutation: E574Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PML, MYL, PP8675, RNF71, TRIM19 / Plasmid: PGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: P29590 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % |
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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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
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: 1.501→37.823 Å / Num. obs: 18492 / % possible obs: 97.56 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 16.41 |
Reflection shell | Resolution: 1.501→1.555 Å / Num. unique obs: 1601 / CC1/2: 0.462 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WJO Resolution: 1.501→37.823 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.33 Å2 / Biso mean: 19.7489 Å2 / Biso min: 8.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.501→37.823 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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