+Open data
-Basic information
Entry | Database: PDB / ID: 1tgz | ||||||
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Title | Structure of human Senp2 in complex with SUMO-1 | ||||||
Components |
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Keywords | CELL CYCLE / HYDROLASE / SUMO / AXAM / SENP / ULP / PROTEASE | ||||||
Function / homology | Function and homology information SUMO-specific endopeptidase activity / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / deSUMOylase activity / 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) / protein desumoylation / nuclear stress granule ...SUMO-specific endopeptidase activity / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / deSUMOylase activity / 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) / protein desumoylation / 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 / regulation of Wnt signaling pathway / 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 / fat cell differentiation / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / mRNA transport / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / negative regulation of protein ubiquitination / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein ubiquitination / positive regulation of protein-containing complex assembly / protein destabilization / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Wnt signaling pathway / Formation of Incision Complex in GG-NER / 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 / protein stabilization / nuclear body / 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: 2.8 Å | ||||||
Authors | Reverter, D. / Lima, C.D. | ||||||
Citation | Journal: Structure / Year: 2004 Title: A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex Authors: Reverter, D. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tgz.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tgz.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/1tgz ftp://data.pdbj.org/pub/pdb/validation_reports/tg/1tgz | HTTPS FTP |
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-Related structure data
-Links
-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: 26787.084 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Details: CHEMICALLY MODIFIED TO PROMOTE BOND BETWEEN CYS548 AND SUMO-1 GLY97 Source: (gene. exp.) Homo sapiens (human) / Gene: SENP2, KIAA1331 / Plasmid: T7 BASED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CP RIL References: UniProt: Q9HC62, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||
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#2: Protein | Mass: 9285.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBL1, SMT3H3, SMT3C / Plasmid: T7 BASED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CP RIL / References: UniProt: P63165 | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 15, 2004 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 16622 / Num. obs: 15675 / % possible obs: 94.3 % / Observed criterion σ(I): -2 / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.8→2.93 Å / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 0.9 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1814230.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.7793 Å2 / ksol: 0.34907 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file |
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