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- PDB-1jd2: Crystal Structure of the yeast 20S Proteasome:TMC-95A complex: A ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jd2 | ||||||
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Title | Crystal Structure of the yeast 20S Proteasome:TMC-95A complex: A non-covalent Proteasome Inhibitor | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / beta-sandwich / proteasome:inhibitor complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Groll, M. / Koguchi, Y. / Huber, R. / Kohno, J. | ||||||
![]() | ![]() Title: Crystal structure of the 20 S proteasome:TMC-95A complex: a non-covalent proteasome inhibitor. Authors: Groll, M. / Koguchi, Y. / Huber, R. / Kohno, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-PROTEASOME COMPONENT ... , 14 types, 28 molecules AVBWCXDYEZF1G2HOIPJQKRLSMTNU
#1: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #2: Protein | Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #3: Protein | Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #4: Protein | Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #5: Protein | Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #6: Protein | Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #7: Protein | Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #8: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #9: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #13: Protein | Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules 89
#15: Protein/peptide |
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-Non-polymers , 2 types, 2903 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#16: Chemical | ChemComp-MG / #17: Water | ChemComp-HOH / | |
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-Details
Compound details | KNOWN AS PROTEASOME INHIBITOR, TMC-95A INHIBITED THE CHYMOTRYPSIN-LIKE (CHT-L), TRYPSIN-LIKE (T-L), ...KNOWN AS PROTEASOME |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.18 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: MPD, MES, DMSO, magnesium Acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 12, 2001 / Details: high intensity beamline |
Radiation | Monochromator: SILICIUM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 742209 / Num. obs: 741075 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 69.354 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 4.22 |
Reflection | *PLUS Num. obs: 255383 / Num. measured all: 741075 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.336 / Rfactor Rwork: 0.271 |