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Yorodumi- PDB-1euv: X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1euv | ||||||
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Title | X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX WITH SMT3, THE YEAST ORTHOLOG OF SUMO. | ||||||
Components |
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Keywords | HYDROLASE / SUMO HYDROLASE / UBIQUITIN-LIKE PROTEASE 1 / SMT3 HYDROLASE DESUMOYLATING ENZYME / CYSTEINE PROTEASE / SUMO PROCESSING ENZYME / SMT3 PROCESSING ENZYME / NABH4 / THIOHEMIACETAL / COVALENT PROTEASE ADDUCT | ||||||
Function / homology | Function and homology information Ulp1 peptidase / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / deSUMOylase activity / protein desumoylation ...Ulp1 peptidase / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / deSUMOylase activity / protein desumoylation / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / Major pathway of rRNA processing in the nucleolus and cytosol / ubiquitin-like protein ligase binding / protein sumoylation / cysteine-type peptidase activity / condensed nuclear chromosome / PML body / protein tag activity / G2/M transition of mitotic cell cycle / nuclear envelope / protein-containing complex binding / nucleolus / proteolysis / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Mossessova, E. / Lima, C.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Authors: Mossessova, E. / Lima, C.D. #1: Journal: Nature / Year: 1999 Title: A New Protease Required for Cell-cycle Progression in Yeast. Authors: Li, S.J. / Hochstrasser, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1euv.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1euv.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 1euv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/1euv ftp://data.pdbj.org/pub/pdb/validation_reports/eu/1euv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer constructed from chain A. / The biological assembly is a monomer constructed from chain B. |
-Components
#1: Protein | Mass: 25650.301 Da / Num. of mol.: 1 / Fragment: C-TERMINAL PROTEASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q02724 |
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#2: Protein | Mass: 9961.278 Da / Num. of mol.: 1 / Fragment: SMT3 RESIDUES 13-98 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306 |
#3: Water | ChemComp-HOH / |
Compound details | Covalent adduct formed between the proteolytic active site thiol and the C-terminal glycine of Smt3 ...Covalent adduct formed between the proteolytic active site thiol and the C-terminal glycine of Smt3 using the reducing agent NaBH4. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.7 % | ||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH6.5, 10% w/v polyethylene glycol 20000, 3% w/v 1,6-hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 221 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. all: 49560 / Num. obs: 47875 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 20.694 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.29 / Num. unique all: 4227 / % possible all: 86 |
Reflection | *PLUS Num. measured all: 449291 |
Reflection shell | *PLUS % possible obs: 86 % / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Resolution: 1.6→25 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Used a -loglikelihood residual derived from Rice distribution for centric and acentric cases of Fs sparse matrix procedure with anisotropic B-factor refinement.
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Refinement step | Cycle: LAST / Resolution: 1.6→25 Å
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Refine LS restraints |
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