+Open data
-Basic information
Entry | Database: PDB / ID: 2iy1 | ||||||
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Title | SENP1 (mutant) full length SUMO1 | ||||||
Components |
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Keywords | HYDROLASE/NUCLEAR PROTEIN / HYDROLASE-NUCLEAR PROTEIN COMPLEX / NUCLEAR PROTEIN / UBL CONJUGATION PATHWAY / PROTEASE / HYDROLASE / UBIQUITIN / THIOL PROTEASE / PROTEIN PROTEIN COMPLEX | ||||||
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 / RHOF GTPase cycle / 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 / regulation of mRNA stability / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / apoptotic signaling pathway / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein stabilization / nuclear body / nuclear speck / focal adhesion / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Shen, L. / Dong, C. / Naismith, J.H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Sumo Protease Senp1 Induces Isomerization of the Scissile Peptide Bond. Authors: Shen, L. / Tatham, M.H. / Dong, C. / Zagorska, A. / Naismith, J.H. / Hay, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iy1.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iy1.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 2iy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/2iy1 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/2iy1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 26900.146 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 419-643 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q9P0U3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein | Mass: 9627.966 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P63165 #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 3.37 Å3/Da / Density % sol: 63.17 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: OSMIC MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→100 Å / Num. obs: 34278 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.46→2.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→40.72 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.884 / SU B: 20.248 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→40.72 Å
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