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Yorodumi- PDB-8oi1: Yeast 20S proteasome in complex with a photoswitchable cepafungin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oi1 | ||||||
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Title | Yeast 20S proteasome in complex with a photoswitchable cepafungin derivative (transCep4) | ||||||
Components |
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Keywords | HYDROLASE / Proteasome / Syrbactins / Photoswitchable Lipid / Binding Analysis | ||||||
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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway ...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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / 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 / 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: 2.95 Å | ||||||
Authors | Morstein, J. / Amatuni, A. / Schuster, A. / Kuttenlochner, W. / Ko, T. / Groll, M. / Adibekian, A. / Renata, H. / Trauner, D.H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024 Title: Optical Control of Proteasomal Protein Degradation with a Photoswitchable Lipopeptide. Authors: Morstein, J. / Amatuni, A. / Shuster, A. / Kuttenlochner, W. / Ko, T. / Abegg, D. / Groll, M. / Adibekian, A. / Renata, H. / Trauner, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oi1.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8oi1.ent.gz | 2.1 MB | Display | PDB format |
PDBx/mmJSON format | 8oi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oi1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8oi1_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8oi1_validation.xml.gz | 205.9 KB | Display | |
Data in CIF | 8oi1_validation.cif.gz | 278.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/8oi1 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/8oi1 | HTTPS FTP |
-Related structure data
Related structure data | 8ohzC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU
#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 #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 #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 #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 #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 #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 |
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-Protein , 1 types, 2 molecules FT
#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 |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#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 #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 #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 #13: Protein | Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30657 #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 , 5 types, 232 molecules
#15: Chemical | ChemComp-MG / #16: Chemical | ChemComp-VOX / ~{ #17: Chemical | #18: Chemical | #19: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2021 |
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: 2.95→30 Å / Num. obs: 214065 / % possible obs: 96.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.95→3.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 20642 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 43.742 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 86.6 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→30 Å
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