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Yorodumi- PDB-1g65: Crystal structure of epoxomicin:20s proteasome reveals a molecula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g65 | |||||||||
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Title | Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity of alpha,beta-epoxyketone proteasome inhibitors | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE inhibitor / proteasome / epoxomicin / ubiquitin / ntn-hydolase / protease / HYDROLASE-HYDROLASE inhibitor complex | |||||||||
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 / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Groll, M. / Kim, K.B. / Kairies, N. / Huber, R. / Crews, C. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2000 Title: Crystal Structure of Epoxomicin:20S Proteasome reveals a molecular basis for selectivity of alpha,beta-Epoxyketone Proteasome Inhibitors Authors: Groll, M. / Kim, K.B. / Kairies, N. / Crews, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g65.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1g65.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 1g65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g65_validation.pdf.gz | 580.4 KB | Display | wwPDB validaton report |
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Full document | 1g65_full_validation.pdf.gz | 754.8 KB | Display | |
Data in XML | 1g65_validation.xml.gz | 137.2 KB | Display | |
Data in CIF | 1g65_validation.cif.gz | 223 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g65 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g65 | 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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Details | one 20S proteasome per asymmetric unit |
-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) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P23639, proteasome endopeptidase complex #2: Protein | Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P23638, proteasome endopeptidase complex #3: Protein | Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P40303, proteasome endopeptidase complex #4: Protein | Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P32379, proteasome endopeptidase complex #5: Protein | Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P40302, proteasome endopeptidase complex #6: Protein | Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P21242, proteasome endopeptidase complex #7: Protein | Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P21243, proteasome endopeptidase complex #8: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P25451, proteasome endopeptidase complex #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P22141, proteasome endopeptidase complex #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P30656, proteasome endopeptidase complex #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P23724, proteasome endopeptidase complex #13: Protein | Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P30657, proteasome endopeptidase complex #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288 References: UniProt: P38624, proteasome endopeptidase complex |
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-Protein/peptide , 1 types, 2 molecules 34
#15: Protein/peptide | Mass: 542.752 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The natural product epoxomicin was isolated from an Actinomycetes strain |
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-Non-polymers , 2 types, 2882 molecules
#16: Chemical | ChemComp-MG / #17: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE STARTING EPOXIDE RING OF EPOXOMICIN (CHAINS 3 AND 4) UNDERGOES RE-CYCLIZATION REACTION WITH THE ...THE STARTING EPOXIDE RING OF EPOXOMICIN |
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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: 3.82 Å3/Da / Density % sol: 67.81 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1M Mes, pH 6.8 11% MPD 25mM MgAc2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 19, 1999 |
Radiation | Monochromator: Silicium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. all: 1336712 / Num. obs: 427960 / % possible obs: 91.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.25→2.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.395 / % possible all: 91.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 1336712 |
Reflection shell | *PLUS Lowest resolution: 2.35 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: wt yeast 20S proteasome (1RYP) Resolution: 2.25→20 Å / σ(F): 3 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 3 / Rfactor obs: 0.283 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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