+Open data
-Basic information
Entry | Database: PDB / ID: 1g0u | ||||||
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Title | A GATED CHANNEL INTO THE PROTEASOME CORE PARTICLE | ||||||
Components | (PROTEASOME COMPONENT ...) x 14 | ||||||
Keywords | HYDROLASE / proteasome / ubiquitin / degradation / protease / Ntn-hydrolase | ||||||
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 / 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Groll, M. / Bajorek, M. / Kohler, A. / Moroder, L. / Rubin, D.M. / Huber, R. / Glickman, M.H. / Finley, D. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: A gated channel into the proteasome core particle. Authors: Groll, M. / Bajorek, M. / Kohler, A. / Moroder, L. / Rubin, D.M. / Huber, R. / Glickman, M.H. / Finley, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g0u.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1g0u.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 1g0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g0u_validation.pdf.gz | 574 KB | Display | wwPDB validaton report |
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Full document | 1g0u_full_validation.pdf.gz | 734.4 KB | Display | |
Data in XML | 1g0u_validation.xml.gz | 132.8 KB | Display | |
Data in CIF | 1g0u_validation.cif.gz | 215.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/1g0u ftp://data.pdbj.org/pub/pdb/validation_reports/g0/1g0u | HTTPS FTP |
-Related structure data
Related structure data | |
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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 biological assembly is a multisubunit complex composed of 28 subunits, whereas 14 subunits are different. |
-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: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P23639, EC: 3.4.99.46 #2: Protein | Mass: 27181.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P23638, EC: 3.4.99.46 #3: Protein | Mass: 27121.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P40303, EC: 3.4.99.46 #4: Protein | Mass: 26453.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P32379, EC: 3.4.99.46 #5: Protein | Mass: 25541.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P40302, EC: 3.4.99.46 #6: Protein | Mass: 27325.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P21242, EC: 3.4.99.46 #7: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P21243, EC: 3.4.99.46 #8: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P25043, EC: 3.4.99.46 #9: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P25451, EC: 3.4.99.46 #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P22141, EC: 3.4.99.46 #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P30656, EC: 3.4.99.46 #12: Protein | Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P23724, EC: 3.4.99.46 #13: Protein | Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P30657, EC: 3.4.99.46 #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P38624, 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: 3.76 Å3/Da / Density % sol: 67.25 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: hanging drop vapor-diffusion / pH: 6.7 Details: 22mM Magnesium acetate, 4% Dimethylsulfoxide, 100mM morpholinoethanesulfonic acid, 11% methylpentanediol, pH 6.7, hanging drop vapour-diffusion, temperature 297K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 378678 / Num. obs: 378678 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 0.2 % / Rmerge(I) obs: 0.396 / % possible all: 85.4 |
Reflection | *PLUS Num. measured all: 1017653 |
Reflection shell | *PLUS Rmerge(I) obs: 0.42 |
-Processing
Software |
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Refinement | Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.25 / Rfactor Rwork: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |