[English] 日本語
Yorodumi- PDB-2ckg: The structure of SENP1 SUMO-2 co-complex suggests a structural ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ckg | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of SENP1 SUMO-2 co-complex suggests a structural basis for discrimination between SUMO paralogues during processing | |||||||||
Components | SENTRIN-SPECIFIC PROTEASE 1 | |||||||||
Keywords | HYDROLASE / PROTEASE / THIOL PROTEASE / NUCLEAR PROTEIN / UBL CONJUGATION PATHWAY | |||||||||
Function / homology | Function and homology information SUMO-specific endopeptidase activity / deSUMOylase activity / SUMO is proteolytically processed / protein desumoylation / RHOF GTPase cycle / protein sumoylation / regulation of mRNA stability / apoptotic signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / nuclear membrane ...SUMO-specific endopeptidase activity / deSUMOylase activity / SUMO is proteolytically processed / protein desumoylation / RHOF GTPase cycle / protein sumoylation / regulation of mRNA stability / apoptotic signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / nuclear membrane / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / positive regulation of transcription by RNA polymerase II / proteolysis / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Dong, C. / Naismith, J.H. | |||||||||
Citation | Journal: Biochem.J. / Year: 2006 Title: The Structure of Senp1-Sumo-2 Complex Suggests a Structural Basis for Discrimination between Sumo Paralogues During Processing. Authors: Shen, L.N. / Dong, C. / Liu, H. / Naismith, J.H. / Hay, R.T. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ckg.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ckg.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ckg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/2ckg ftp://data.pdbj.org/pub/pdb/validation_reports/ck/2ckg | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ckhC 2bkqS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
|
-Components
#1: Protein | Mass: 26803.098 Da / Num. of mol.: 2 / Fragment: RESIDUES 419-643 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: Water | ChemComp-HOH / | Compound details | DEGRADES UBL1 AND SMT3H2 CONJUGATES | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.59 % |
---|---|
Crystal grow | pH: 4.5 / Details: pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ACSD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→54 Å / Num. obs: 21832 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BKQ Resolution: 2.45→66.96 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 21.67 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 66.96 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→66.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|