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Yorodumi- PDB-9ey9: Yeast 20S proteasome in complex with a sybactin derivative (PheSyr) -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9ey9 | ||||||
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| Title | Yeast 20S proteasome in complex with a sybactin derivative (PheSyr) | ||||||
Components |
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Keywords | HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Syrbactins / Natural Product Derivative / Binding Analysis | ||||||
| Function / homology | Function and homology informationproteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / 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 / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / Ub-specific processing proteases / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / proteasome complex / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Praeve, L. / Kuttenlochner, W. / Tabak, W.W.A. / Langer, C. / Kaiser, M. / Groll, M. / Bode, H.B. | ||||||
| Funding support | Germany, 1items
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Citation | Journal: Chem / Year: 2024Title: Bioengineering of syrbactin megasynthetases for immunoproteasome inhibitor production Authors: Prave, L. / Kuttenlochner, W. / Tabak, W.W. / Langer, C. / Kaiser, M. / Groll, M. / Bode, H.B. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9ey9.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9ey9.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9ey9.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9ey9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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| Full document | 9ey9_full_validation.pdf.gz | 1.6 MB | Display | |
| Data in XML | 9ey9_validation.xml.gz | 225.4 KB | Display | |
| Data in CIF | 9ey9_validation.cif.gz | 289 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/9ey9 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/9ey9 | HTTPS FTP |
-Related structure data
| Related structure data | |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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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) ![]() #2: Protein | Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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) ![]() |
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-Proteasome endopeptidase ... , 2 types, 4 molecules HVKY
| #8: Protein | Mass: 25013.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: A0A6A5Q449, proteasome endopeptidase complex #11: Protein | Mass: 23224.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: A0A6A5Q5W3, proteasome endopeptidase complex |
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-Proteasome subunit beta type- ... , 5 types, 10 molecules IWJXLZMaNb
| #9: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P38624, proteasome endopeptidase complex |
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-Non-polymers , 2 types, 12 molecules 
| #15: Chemical | ChemComp-MG / #16: Chemical | ChemComp-A1H71 / Mass: 603.750 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H49N5O7 / Feature type: SUBJECT OF INVESTIGATION |
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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: 3.73 Å3/Da / Density % sol: 66.99 % |
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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: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å |
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2023 |
| Radiation | Monochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
| Reflection | Resolution: 3.1→30 Å / Num. obs: 194950 / % possible obs: 98.4 % / Redundancy: 30 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.4 |
| Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.691 / Num. unique obs: 17800 / % possible all: 99.4 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 61.832 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / 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: 100.593 Å2
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| Refinement step | Cycle: 1 / Resolution: 3.1→30 Å
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| Refine LS restraints |
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X-RAY DIFFRACTION
Germany, 1items
Citation
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