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Yorodumi- PDB-1fnt: CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST IN COMPLEX WIT... -
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-Basic information
Entry | Database: PDB / ID: 1fnt | ||||||
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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 / MULTICATALYTIC PROTEINASE / 20S PROTEASOME / PROTEIN DEGRADATION / ANTIGEN PROCESSING / PROTEASE / PROTEASOME ACTIVATOR / CELL ADHESION / INTERFERON INDUCTION / 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 / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly ...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 / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / proteolysis / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Whitby, F.G. / Masters, E. / Kramer, L. / Knowlton, J.R. / Yao, Y. / Wang, C.C. / Hill, C.P. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Structural basis for the activation of 20S proteasomes by 11S regulators. Authors: Whitby, F.G. / Masters, E.I. / Kramer, L. / Knowlton, J.R. / Yao, Y. / Wang, C.C. / Hill, C.P. | ||||||
History |
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Remark 300 | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 42 CHAIN(S). SEE REMARK ... THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 42 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). YEAST PROTEASOME IS COMPOSED OF 14 DIFFERENT SUBUNITS WHICH FORM A HIGHLY ORDERED RING-SHAPED STRUCTURE. PA26 IS A HEPTAMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fnt.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1fnt.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 1fnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/1fnt ftp://data.pdbj.org/pub/pdb/validation_reports/fn/1fnt | HTTPS FTP |
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-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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-Components
-PROTEASOME COMPONENT ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZMaNb
#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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #3: Protein | Mass: 27181.609 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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #7: Protein | Mass: 31443.875 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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #9: Protein | Mass: 25114.459 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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #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, EC: 3.4.99.46 #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, EC: 3.4.99.46 |
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-Protein / Non-polymers , 2 types, 28 molecules cdefghijklmnop
#15: Protein | Mass: 25272.787 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 #16: Chemical | ChemComp-MG / |
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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: 60.05 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M NaHEPES, 40% MPD, 0.2 M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000 / Details: SSRL/9-1 |
Radiation | Monochromator: SSRL/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. obs: 189495 / % possible obs: 89.1 % / 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: 62.9 |
Reflection | *PLUS Num. measured all: 503540 |
Reflection shell | *PLUS % possible obs: 62.9 % / Num. unique obs: 6632 / Num. measured obs: 16790 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1/2 OF 20S PROTEASOME INCLUDING ALPHA-1-7 AND REMARK 200 BETA-1-7, REDUCED TO A POLY-ALANINE MODEL. Resolution: 3.2→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: NCS RESTRAINTS APPLIED CONSIDERING THE 14-FOLD SYMMETRY OF PA26 IN THE ASYMMETRIC UNIT AND THE 2-FOLD SYMMETRY OF 20S PROTEASOME
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Displacement parameters | Biso mean: 83 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.35 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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