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- PDB-1yar: Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yar | ||||||
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Title | Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex | ||||||
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![]() | HYDROLASE/HYDROLASE ACTIVATOR / proteasome 20S / PA26 proteasome activator 11S / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX | ||||||
Function / homology | ![]() proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteolysis ...proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forster, A. / Masters, E.I. / Whitby, F.G. / Robinson, H. / Hill, C.P. | ||||||
![]() | ![]() 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 For the Proteasome beta subunit (chains H,I,J,K,L,M,N) the first 8 residues are cleaved ...SEQUENCE For the Proteasome beta subunit (chains H,I,J,K,L,M,N) the first 8 residues are cleaved off autocatalytically during assembly of the complex. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 945.4 KB | Display | ![]() |
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PDB format | ![]() | 784.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 649.5 KB | Display | ![]() |
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Full document | ![]() | 716.5 KB | Display | |
Data in XML | ![]() | 196.2 KB | Display | |
Data in CIF | ![]() | 278.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ya7C ![]() 1yauC ![]() 1z7qC ![]() 1pmaS C: citing same article ( 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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1 | ![]()
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Unit cell |
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Details | T. acidophilum is a 28-subunit barrel-shaped complex. It contains 2 stacked homoheptameric rings of beta subunits flanked by 2 homoheptameric rings of alpha subunits. One half of the 20S complex is contained in the asymmetric unit (one ring of beta and one ring of alpha subunits. / PA26 is a homoheptameric ring that binds to the end of the 20S proteasome through interactions with the 20S alpha subunits. One PA26 complex is contained in the asymmetric unit. |
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Components
-Protein , 3 types, 21 molecules ABCDEFGHIJKLMNOPQRSTU
#1: Protein | Mass: 25801.439 Da / Num. of mol.: 7 / Mutation: D9S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P25156, proteasome endopeptidase complex #2: Protein | Mass: 23998.691 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P28061, proteasome endopeptidase complex #3: Protein | Mass: 26087.643 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 3 types, 3498 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
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![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.1M Na-citrate/phosphate buffer, 0.2M Lithium Sulfate, 15% PEG-1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 442007 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1PMA Resolution: 1.9→47.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.843 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.131 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.532 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.899→1.949 Å / Total num. of bins used: 20
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