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Yorodumi- PDB-1ryp: CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST AT 2.4 ANGSTRO... -
+Open data
-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 | ||||||
Components | (20S PROTEASOME) x 14 | ||||||
Keywords | MULTICATALYTIC PROTEINASE / 20S PROTEASOME / PROTEIN DEGRADATION / ANTIGEN PROCESSING / HYDROLASE / PROTEASE | ||||||
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 / 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 / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Groll, M. / Ditzel, L. / Loewe, J. / Stock, D. / Bochtler, M. / Bartunik, H.D. / Huber, R. | ||||||
Citation | Journal: Nature / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ryp.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1ryp.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 1ryp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ryp_validation.pdf.gz | 544.6 KB | Display | wwPDB validaton report |
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Full document | 1ryp_full_validation.pdf.gz | 643.9 KB | Display | |
Data in XML | 1ryp_validation.xml.gz | 122.8 KB | Display | |
Data in CIF | 1ryp_validation.cif.gz | 203.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/1ryp ftp://data.pdbj.org/pub/pdb/validation_reports/ry/1ryp | HTTPS FTP |
-Related structure data
Related structure data | 1pmaS S: Starting model for refinement |
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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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-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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21243, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23639, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23638, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40303, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32379, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40302, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21242, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38624, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25043, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25451, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22141, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30656, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23724, EC: 3.4.99.46 #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) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30657, EC: 3.4.99.46 |
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-Non-polymers , 2 types, 2928 molecules
#15: Chemical | ChemComp-MG / #16: Water | ChemComp-HOH / | |
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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: 3.53 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: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 |
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 |
-Processing
Software |
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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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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