+Open data
-Basic information
Entry | Database: PDB / ID: 2iy0 | ||||||
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Title | SENP1 (mutant) SUMO1 RanGAP | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE ACTIVATOR / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX / HYDROLASE-ACTIVATOR COMPLEX / PROTEASE / HYDROLASE / UBIQUITIN / THIOL PROTEASE / LEUCINE- RICH REPEAT / UBL CONJUGATION PATHWAY / PROTEIN PROTEIN COMPLEX / GTPASE ACTIVATION / HYDROLASE-ACTIVATOR COMPLEX UBL CONJUGATION / NUCLEAR PROTEIN / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information SUMO-specific endopeptidase activity / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / 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-specific endopeptidase activity / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / 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) / nuclear pore cytoplasmic filaments / 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 / nuclear export / Maturation of nucleoprotein / Rev-mediated nuclear export of HIV RNA / activation of GTPase activity / negative regulation of protein export from nucleus / SUMOylation of RNA binding proteins / aggresome / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / 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 / response to axon injury / potassium channel regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Resolution of Sister Chromatid Cohesion / cellular response to cadmium ion / regulation of mRNA stability / SUMOylation of chromatin organization proteins / GTPase activator activity / SUMOylation of transcription cofactors / RHO GTPases Activate Formins / 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 / mitotic spindle / protein tag activity / kinetochore / small GTPase binding / Formation of Incision Complex in GG-NER / Separation of Sister Chromatids / 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 envelope / nuclear membrane / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein stabilization / nuclear body / nuclear speck / cadherin binding / focal adhesion / DNA repair / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / dendrite / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / enzyme binding / signal transduction / 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: 2.77 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 | 2iy0.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iy0.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 2iy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/2iy0 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/2iy0 | HTTPS FTP |
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-Related 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: 26900.146 Da / Num. of mol.: 1 / 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 |
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#2: Protein | Mass: 9524.822 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) / References: UniProt: P63165 |
#3: Protein | Mass: 17141.896 Da / Num. of mol.: 1 / Fragment: C-TERMINUS, RESIDUES 432-587 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P46060 |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 49.9 % |
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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: 2.77→38 Å / Num. obs: 13161 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.77→2.87 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→37.35 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.872 / SU B: 36.217 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→37.35 Å
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