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Yorodumi- PDB-6uyy: Crystal structure of K39-acetylated SUMO1 in complex with phospho... -
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-Basic information
Entry | Database: PDB / ID: 6uyy | |||||||||
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Title | Crystal structure of K39-acetylated SUMO1 in complex with phosphorylated DAXX | |||||||||
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 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 / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding ...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 / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Formation of Incision Complex in GG-NER / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / protein stabilization / nuclear body / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 | 6uyy.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uyy.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 6uyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/6uyy ftp://data.pdbj.org/pub/pdb/validation_reports/uy/6uyy | HTTPS FTP |
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-Related structure data
Related structure data | 6uyoC 6uypC 6uyqC 6uyrC 6uysC 6uytC 6uyuC 6uyvC 6uyxC 6uyzC 4wjnS 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 on special symmetry positions |
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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P63165 |
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#2: Protein/peptide | Mass: 2000.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#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: 2.05 Å3/Da / Density % sol: 39.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100MM SODIUM CACODYLATE PH6.5, 26% PEG3350, 10MM CALCIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9775 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→19.081 Å / Num. obs: 11903 / % possible obs: 95.17 % / Redundancy: 3.3 % / CC1/2: 0.998 / Net I/σ(I): 10.67 |
Reflection shell | Resolution: 1.599→1.656 Å / Num. unique obs: 901 / CC1/2: 0.714 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WJN Resolution: 1.599→19.081 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.42 Å2 / Biso mean: 27.6282 Å2 / Biso min: 10.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.599→19.081 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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