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Yorodumi- PDB-9fsu: Yeast 20S proteasome with human beta1i (1-51) in complex with epo... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9fsu | ||||||
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| Title | Yeast 20S proteasome with human beta1i (1-51) in complex with epoxyketone inhibitor 16 | ||||||
Components |
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Keywords | HYDROLASE / Proteasome / Mutant / Human Chimeric Subunit / Structure-based Drug Development / Inhibitor / Binding Analysis | ||||||
| Function / homology | Function and homology informationspermatoproteasome complex / Proteasome assembly / proteasome core complex / 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 ...spermatoproteasome complex / Proteasome assembly / proteasome core complex / 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 / immune system process / 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 / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
| Biological species | Homo sapiens (human)![]() synthetic construct (others) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Maurits, E. / Huber, E.M. / Dekker, P.M. / Wang, X. / Heinemeyer, W. / Florea, B.I. / Groll, M. / Overkleeft, H.S. | ||||||
| Funding support | Germany, 1items
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Citation | Journal: To Be PublishedTitle: Structure-based design of peptide epoxyketones selectively targeting the three human immunoproteasome active sites Authors: Maurits, E. / Huber, E.M. / Dekker, P.M. / Wang, X. / Heinemeyer, W. / Florea, B.I. / Groll, M. / Overkleeft, H.S. | ||||||
| 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 | 9fsu.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9fsu.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9fsu.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9fsu_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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| Full document | 9fsu_full_validation.pdf.gz | 2.2 MB | Display | |
| Data in XML | 9fsu_validation.xml.gz | 240.5 KB | Display | |
| Data in CIF | 9fsu_validation.cif.gz | 311.6 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/9fsu ftp://data.pdbj.org/pub/pdb/validation_reports/fs/9fsu | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9frwC ![]() 9fstC ![]() 9fsvC ![]() 9ft0C ![]() 9ft1C C: citing same article ( |
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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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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 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) ![]() 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) ![]() #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 23224.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() 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) ![]() #13: Protein | Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 21369.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) ![]() Gene: PSMB9, LMP2, PSMB6i, RING12, PRE3, YJL001W, J1407 / Production host: ![]() References: UniProt: P28065, UniProt: P38624, proteasome endopeptidase complex |
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-Non-polymers , 6 types, 283 molecules 








| #15: Chemical | ChemComp-MG / #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-SO4 / #19: Chemical | ChemComp-A1IFL / ( Mass: 719.865 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H57N5O10 / Source: (synth.) synthetic construct (others) / Feature type: SUBJECT OF INVESTIGATION #20: 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: 3.74 Å3/Da / Density % sol: 67.15 % |
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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: Nov 27, 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: 2.75→30 Å / Num. obs: 269777 / % possible obs: 97 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.3 |
| Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / Num. unique obs: 27968 / % possible all: 99.1 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 37.864 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.538 / ESU R Free: 0.306 / 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: 78.049 Å2
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| Refinement step | Cycle: 1 / Resolution: 2.75→30 Å
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| Refine LS restraints |
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
Germany, 1items
Citation





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