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Yorodumi- PDB-3gpj: Crystal structure of the yeast 20S proteasome in complex with syr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gpj | ||||||
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Title | Crystal structure of the yeast 20S proteasome in complex with syringolin B | ||||||
Components | (Proteasome component ...) x 14 | ||||||
Keywords | HYDROLASE / Proteasome / virulence / ubiquitin / cancer therapy / immunology / Cytoplasm / Nucleus / Phosphoprotein / Protease / Threonine protease / Isopeptide bond / Ubl conjugation / Zymogen | ||||||
Function / homology | Function and homology information proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Groll, M. / Huber, R. / Kaiser, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition Authors: Clerc, J. / Groll, M. / Illich, D.J. / Bachmann, A.S. / Huber, R. / Schellenberg, B. / Dudler, R. / Kaiser, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gpj.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3gpj.ent.gz | 1017.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gpj_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3gpj_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3gpj_validation.xml.gz | 251.8 KB | Display | |
Data in CIF | 3gpj_validation.cif.gz | 340.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/3gpj ftp://data.pdbj.org/pub/pdb/validation_reports/gp/3gpj | HTTPS FTP |
-Related structure data
Related structure data | 1rypS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Proteasome component ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2
#1: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23639, proteasome endopeptidase complex #2: Protein | Mass: 27050.416 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-245 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23638, proteasome endopeptidase complex #3: Protein | Mass: 26903.330 Da / Num. of mol.: 2 / Fragment: sequence database residues 3-243 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P40303, proteasome endopeptidase complex #4: Protein | Mass: 26544.789 Da / Num. of mol.: 2 / Fragment: sequence database residues 9-250 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P32379, proteasome endopeptidase complex #5: Protein | Mass: 25502.805 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-234 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P40302, proteasome endopeptidase complex #6: Protein | Mass: 26892.482 Da / Num. of mol.: 2 / Fragment: sequence database residues 5-248 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21242, proteasome endopeptidase complex #7: Protein | Mass: 27316.037 Da / Num. of mol.: 2 / Fragment: sequence database residues 10-252 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21243, proteasome endopeptidase complex #8: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Fragment: sequence database residues 30-251 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-205 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P25451, proteasome endopeptidase complex #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-198 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P22141, proteasome endopeptidase complex #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Fragment: sequence database residues 76-287 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P30656, proteasome endopeptidase complex #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Fragment: sequence database residues 20-241 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23724, proteasome endopeptidase complex #13: Protein | Mass: 25945.496 Da / Num. of mol.: 2 / Fragment: sequence database residues 34-266 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P30657, proteasome endopeptidase complex #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Fragment: sequence database residues 20-215 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P38624, proteasome endopeptidase complex |
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-Non-polymers , 2 types, 1339 molecules
#15: Chemical | ChemComp-SY2 / #16: Water | ChemComp-HOH / | |
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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: 3.78 Å3/Da / Density % sol: 67.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 12% MPD, 0.1M MES, pH 6.7, 20mM MgAc2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2007 / Details: SINGLE BOUNCE MULTILAYER OPTIC |
Radiation | Monochromator: double bounce Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. all: 285204 / Num. obs: 282923 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.154 |
Reflection shell | Resolution: 2.7→2.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.9 / Num. unique all: 42826 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ryp Resolution: 2.7→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 71944.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.716 Å2 / ksol: 0.349924 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 38.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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