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- PDB-1ryp: CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST AT 2.4 ANGSTRO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ryp | ||||||
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Title | CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST AT 2.4 ANGSTROMS RESOLUTION | ||||||
![]() | (20S PROTEASOME) x 14 | ||||||
![]() | MULTICATALYTIC PROTEINASE / 20S PROTEASOME / PROTEIN DEGRADATION / ANTIGEN PROCESSING / HYDROLASE / PROTEASE | ||||||
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 / threonine-type endopeptidase activity / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / 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. / Ditzel, L. / Loewe, J. / Stock, D. / Bochtler, M. / Bartunik, H.D. / Huber, R. | ||||||
![]() | ![]() Title: Structure of 20S proteasome from yeast at 2.4 A resolution. Authors: Groll, M. / Ditzel, L. / Lowe, J. / Stock, D. / Bochtler, M. / Bartunik, H.D. / Huber, R. | ||||||
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
Summary document | ![]() | 544.6 KB | Display | ![]() |
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Full document | ![]() | 643.9 KB | Display | |
Data in XML | ![]() | 122.8 KB | Display | |
Data in CIF | ![]() | 203.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pmaS S: Starting model for refinement |
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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
-Protein , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2
#1: Protein | Mass: 27316.037 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 27050.416 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 26903.330 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 26544.789 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 25502.805 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 26892.482 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 22401.266 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 23353.262 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 25945.496 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 2 types, 2928 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#15: Chemical | ChemComp-MG / #16: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.9 / Details: pH 6.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 778118 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 2 |
Reflection shell | Highest resolution: 1.97 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2 / % possible all: 93.6 |
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Processing
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Refinement | Starting model: PDB ENTRY 1PMA Resolution: 1.9→50 Å / Rfactor Rfree error: 0 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Displacement parameters | Biso mean: 36.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 2 Å2 / Rms dev position: 0.15 Å / Weight Biso : 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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