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Yorodumi- PDB-1z7q: Crystal structure of the 20s proteasome from yeast in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z7q | ||||||
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Title | Crystal structure of the 20s proteasome from yeast in complex with the proteasome activator PA26 from Trypanosome brucei at 3.2 angstroms resolution | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE ACTIVATOR / 20S / proteasome / PA26 / activator / multi-catalytic protease / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX | ||||||
Function / homology | Function and homology information proteasome activator complex / 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 ...proteasome activator complex / 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 / Ub-specific processing proteases / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / peroxisome / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / proteolysis / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å | ||||||
Authors | Forster, A. / Whitby, F.G. / Hill, C.P. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Authors: Forster, A. / Masters, E.I. / Whitby, F.G. / Robinson, H. / Hill, C.P. | ||||||
History |
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Remark 999 | SEQUENCE Residue (i GLY 1172) and Residue (i GLY 1173) are not linked. Distance of C-N bond is 1.91. ...SEQUENCE Residue (i GLY 1172) and Residue (i GLY 1173) are not linked. Distance of C-N bond is 1.91. Residue (p GLY 1172) and Residue (p GLY 1173) are not linked. Distance of C-N bond is 1.91. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z7q.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1z7q.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 1z7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z7q_validation.pdf.gz | 727.1 KB | Display | wwPDB validaton report |
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Full document | 1z7q_full_validation.pdf.gz | 861.9 KB | Display | |
Data in XML | 1z7q_validation.xml.gz | 291 KB | Display | |
Data in CIF | 1z7q_validation.cif.gz | 399 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/1z7q ftp://data.pdbj.org/pub/pdb/validation_reports/z7/1z7q | HTTPS FTP |
-Related structure data
Related structure data | 1ya7C 1yarC 1yauC 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 | 1 complete, 28-subunit 20S proteasome is found in the asymmetric unit / 2 complete, 7-subunit PA26 compllexes are found in the asymmetric unit |
-Components
-Proteasome component ... , 13 types, 26 molecules AOBPCQDRESFTGUHVIWJXKYLZNb
#1: Protein | Mass: 28033.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21243, proteasome endopeptidase complex #2: Protein | Mass: 27191.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23639, proteasome endopeptidase complex #3: Protein | Mass: 28748.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23638, proteasome endopeptidase complex #4: Protein | Mass: 28478.111 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P40303, proteasome endopeptidase complex #5: Protein | Mass: 28649.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P32379, proteasome endopeptidase complex #6: Protein | Mass: 25634.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P40302, proteasome endopeptidase complex #7: Protein | Mass: 31575.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21242, proteasome endopeptidase complex #8: Protein | Mass: 21517.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P38624, proteasome endopeptidase complex #9: Protein | Mass: 23987.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P25043, proteasome endopeptidase complex #10: Protein | Mass: 22627.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P25451, proteasome endopeptidase complex #11: Protein | Mass: 22545.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P22141, proteasome endopeptidase complex #12: Protein | Mass: 23353.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P30656, proteasome endopeptidase complex #14: Protein | Mass: 25945.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P30657, proteasome endopeptidase complex |
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-Protein , 2 types, 16 molecules Macdefghijklmnop
#13: Protein | Mass: 24883.928 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23724, proteasome endopeptidase complex #15: Protein | Mass: 25228.734 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U8G2 |
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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: 3.08 Å3/Da / Density % sol: 60.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M NaHEPES, 40% MPD, 0.2 M NACL, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000 |
Radiation | Monochromator: SSRL beamline 9-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 189615 / Num. obs: 189615 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.331 / % possible all: 0.0629 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: one-half of the yeast 20S proteasome (Huber, et al., high-resolution structure), pdb entry 1RYP Resolution: 3.22→39.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.22→39.8 Å
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