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Yorodumi- PDB-5aek: Crystal structure of the human SENP2 C548S in complex with the hu... -
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-Basic information
Entry | Database: PDB / ID: 5aek | ||||||
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Title | Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W | ||||||
Components |
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Keywords | HYDROLASE / SUMO / SENP / FOLDING EVOLUTION | ||||||
Function / homology | Function and homology information SUMO-specific endopeptidase activity / protein localization to nuclear pore / 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) / deSUMOylase activity / nuclear stress granule ...SUMO-specific endopeptidase activity / protein localization to nuclear pore / 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) / deSUMOylase activity / nuclear stress granule / protein desumoylation / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / regulation of Wnt signaling pathway / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of chromatin organization proteins / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / roof of mouth development / ubiquitin-specific protease binding / fat cell differentiation / negative regulation of DNA binding / ubiquitin-like protein ligase binding / transcription factor binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / cellular response to cadmium ion / potassium channel regulator activity / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / negative regulation of protein ubiquitination / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / positive regulation of protein ubiquitination / protein destabilization / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Wnt signaling pathway / Formation of Incision Complex in GG-NER / protein tag activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / nuclear body / protein stabilization / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Gallego, P. / Grana-Montes, R. / Espargaro, A. / Castillo, V. / Torrent, J. / Lange, R. / Papaleo, E. / Lindorff-Larsend, K. / Ventura, S. / Reverter, D. | ||||||
Citation | Journal: To be Published Title: Stepping Back and Forward on Sumo Folding Evolution Authors: Grana-Montes, R. / Gallego, P. / Espargaro, A. / Castillo, V. / Torrent, J. / Lange, R. / Reverter, D. / Papaleo, E. / Lindorff-Larsend, K. / Ventura, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aek.cif.gz | 707.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aek.ent.gz | 594.1 KB | Display | PDB format |
PDBx/mmJSON format | 5aek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aek_validation.pdf.gz | 617.4 KB | Display | wwPDB validaton report |
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Full document | 5aek_full_validation.pdf.gz | 768.6 KB | Display | |
Data in XML | 5aek_validation.xml.gz | 134.4 KB | Display | |
Data in CIF | 5aek_validation.cif.gz | 181.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aek ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aek | HTTPS FTP |
-Related structure data
Related structure data | 1tgzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 26542.773 Da / Num. of mol.: 12 / Fragment: CATALYTIC DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HC62, Ulp1 peptidase #2: Protein | Mass: 9140.415 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P63165 |
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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: 3.14 Å3/Da / Density % sol: 60.79 % / Description: NONE |
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Crystal grow | Temperature: 291 K Details: 2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979491 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979491 Å / Relative weight: 1 |
Reflection | Resolution: 3→46.76 Å / Num. obs: 101157 / % possible obs: 94.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.4 / % possible all: 87.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TGZ Resolution: 3→47 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.835 / SU B: 24.349 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.789 Å2
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Refinement step | Cycle: LAST / Resolution: 3→47 Å
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