[English] 日本語
![](img/lk-miru.gif)
- PDB-3dy3: Crystal structure of yeast 20S proteasome in complex with the epi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3dy3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of yeast 20S proteasome in complex with the epimer form of spirolactacystin | ||||||
![]() | (Proteasome component ...) x 14 | ||||||
![]() | HYDROLASE / Proteasome / Inhibitor / Protein Degradation / Ubiquitin-Proteasome-Pathway / Cytoplasm / Nucleus / Protease / Threonine protease / Ubl conjugation / Phosphoprotein / Zymogen | ||||||
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. / Balskus, E. / Jacobsen, E. | ||||||
![]() | ![]() Title: Structural analysis of spiro beta-lactone proteasome inhibitors. Authors: Groll, M. / Balskus, E.P. / Jacobsen, E.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1006.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3dy4C ![]() 1rypS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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 Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P23639, proteasome endopeptidase complex #2: Protein | Mass: 27050.416 Da / Num. of mol.: 2 / Fragment: UNP residues 2-245 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P23638, proteasome endopeptidase complex #3: Protein | Mass: 26903.330 Da / Num. of mol.: 2 / Fragment: UNP residues 3-243 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P40303, proteasome endopeptidase complex #4: Protein | Mass: 26544.789 Da / Num. of mol.: 2 / Fragment: UNP residues 9-250 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P32379, proteasome endopeptidase complex #5: Protein | Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P40302, proteasome endopeptidase complex #6: Protein | Mass: 26892.482 Da / Num. of mol.: 2 / Fragment: UNP residues 5-248 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P21242, proteasome endopeptidase complex #7: Protein | Mass: 27316.037 Da / Num. of mol.: 2 / Fragment: UNP residues 10-252 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P21243, proteasome endopeptidase complex #8: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Fragment: UNP residues 30-251 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P25451, proteasome endopeptidase complex #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P22141, proteasome endopeptidase complex #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Fragment: UNP residues 76-287 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P30656, proteasome endopeptidase complex #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Fragment: UNP residues 20-241 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P23724, proteasome endopeptidase complex #13: Protein | Mass: 25945.496 Da / Num. of mol.: 2 / Fragment: UNP residues 34-266 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P30657, proteasome endopeptidase complex #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Fragment: UNP residues 20-215 / Source method: isolated from a natural source Details: 20S proteasome was prepared from yeast under native conditions Source: (natural) ![]() ![]() References: UniProt: P38624, proteasome endopeptidase complex |
---|
-Non-polymers , 2 types, 1008 molecules ![](data/chem/img/SLR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#15: Chemical | #16: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | SPIROLACTASYSTIN EPIMER IS COVALENTLY BOUND TO THR1 OF SUBUNITS BETA1, BETA2 AND BETA5 BY ESTER ...SPIROLACTA |
---|---|
Sequence details | PROTEASOME |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.03 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1 M MES, 10 % MPD, 20 mM MgAc2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2007 |
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: 2.81→99 Å / Num. all: 257298 / Num. obs: 252667 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 2.81→2.85 Å / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1RYP Resolution: 2.81→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3376056.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.1434 Å2 / ksol: 0.361889 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.81→2.97 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|