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Yorodumi- PDB-3nzj: Crystal structure of yeast 20S proteasome in complex with ligand 2a -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nzj | ||||||
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Title | Crystal structure of yeast 20S proteasome in complex with ligand 2a | ||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / ubiquitin / protein degradation / N-terminal nucleophilic hydrolase / 19S regulatory particle / ubiquitin-tagged substrates / cytosol / nucleus / 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 / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / Ub-specific processing proteases ...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 / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / Ub-specific processing proteases / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Groll, M. / Gallastegui, N. / Marechal, X. / Le Ravalec, V. / Basse, N. / Richy, N. / Genin, E. / Huber, R. / Moroder, M. / Vidal, V. / Reboud-Ravaux, M. | ||||||
Citation | Journal: Chemmedchem / Year: 2010 Title: 20S proteasome inhibition: designing noncovalent linear peptide mimics of the natural product TMC-95A. Authors: Groll, M. / Gallastegui, N. / Marechal, X. / Le Ravalec, V. / Basse, N. / Richy, N. / Genin, E. / Huber, R. / Moroder, L. / Vidal, J. / Reboud-Ravaux, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nzj.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3nzj.ent.gz | 1019 KB | Display | PDB format |
PDBx/mmJSON format | 3nzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/3nzj ftp://data.pdbj.org/pub/pdb/validation_reports/nz/3nzj | HTTPS FTP |
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-Related structure data
Related structure data | 3nzwC 3nzxC 1rypS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains the dimeric 20S proteasome, composed of 28 subunits with 7 different alpha- and seven different beta-type subunits |
-Components
-Proteasome component ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2
#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: 28299.889 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: 31670.539 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: 26905.076 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: 29471.289 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: 23573.604 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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-Protein/peptide , 1 types, 2 molecules 34
#15: Protein/peptide |
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-Non-polymers , 2 types, 1338 molecules
#16: Chemical | #17: Water | ChemComp-HOH / | |
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-Details
Compound details | THE ENTIRE CHAIN OF 3 OR 4 IS THE POLYMER REPRESENTATION OF THE INHIBITOR COMPOUND UNDER THE ...THE ENTIRE CHAIN OF 3 OR 4 IS THE POLYMER REPRESENTA |
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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: 3.56 Å3/Da / Density % sol: 65.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 1000 mM MES / HCl, 6.8, 12% MPD, 20 mM MgAc2, 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: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2009 |
Radiation | Monochromator: Focusing Spherical Grating Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 415965 / Num. obs: 415923 / % possible obs: 99.5 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 2.5 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RYP Resolution: 2.4→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 6201975.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.5 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 4.37195 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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