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Yorodumi- PDB-4j70: Yeast 20S proteasome in complex with the belactosin derivative 3e -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j70 | ||||||
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Title | Yeast 20S proteasome in complex with the belactosin derivative 3e | ||||||
Components | (Proteasome component ...) x 14 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Proteasome / drug discovery / irreversible inhibition / beta-lactone / Ntn hydrolase / 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 / Ub-specific processing proteases / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / 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: 2.8 Å | ||||||
Authors | Kawamura, S. / Unno, Y. / List, A. / Tanaka, M. / Sasaki, T. / Arisawa, M. / Asai, A. / Groll, M. / Shuto, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Potent Proteasome Inhibitors Derived from the Unnatural cis-Cyclopropane Isomer of Belactosin A: Synthesis, Biological Activity, and Mode of Action. Authors: Kawamura, S. / Unno, Y. / List, A. / Mizuno, A. / Tanaka, M. / Sasaki, T. / Arisawa, M. / Asai, A. / Groll, M. / Shuto, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j70.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4j70.ent.gz | 1021.4 KB | Display | PDB format |
PDBx/mmJSON format | 4j70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j70_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4j70_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4j70_validation.xml.gz | 210.7 KB | Display | |
Data in CIF | 4j70_validation.cif.gz | 300.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/4j70 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j70 | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
NCS oper:
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-Components
-Proteasome component ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZMaNb
#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: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23638, proteasome endopeptidase complex #3: Protein | Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P40303, proteasome endopeptidase complex #4: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P32379, proteasome endopeptidase complex #5: Protein | Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P40302, proteasome endopeptidase complex #6: Protein | Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21242, proteasome endopeptidase complex #7: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21243, proteasome endopeptidase complex #8: Protein | Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / 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 / 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 / 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 / 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 / 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 / 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, 1338 molecules
#15: Chemical | Type: Peptide-like / Class: Inhibitor / Mass: 565.700 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H43N3O6 References: BENZYL [(2S)-1-({(2R)-1-[(1S,2S)-2-{[(2R,3S,4S)-3-FORMYL-2-HYDROXY-4-METHYLHEXANOYL]AMINO}CYCLOPROPYL]-4-PHENYLBUTAN-2-YL}AMINO)-1-OXOPROPAN-2-YL]CARBAMATE #16: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 3.8 Å3/Da / Density % sol: 67.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 20 mM magnesium acetate, 0.1 M MES, 12% MPD, pH 6.9, 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 9, 2011 |
Radiation | Monochromator: LN2-cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. all: 266454 / Num. obs: 262724 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.474 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RYP Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.723 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.473 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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