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- PDB-1ya7: Implications for interactions of proteasome with PAN and PA700 fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ya7 | ||||||
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Title | Implications for interactions of proteasome with PAN and PA700 from the 1.9 A structure of a proteasome-11S activator complex | ||||||
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![]() | HYDROLASE/HYDROLASE ACTIVATOR / archaeal proteasome / PA26 / copmlex / open gate / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX | ||||||
Function / homology | ![]() proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / 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 / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 888.5 KB | Display | ![]() |
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PDB format | ![]() | 738.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 650.4 KB | Display | ![]() |
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Full document | ![]() | 734.4 KB | Display | |
Data in XML | ![]() | 173.4 KB | Display | |
Data in CIF | ![]() | 236.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yarC ![]() 1yauC ![]() 1z7qC ![]() 1pmaS S: Starting model for refinement C: citing same article ( |
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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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Components on special symmetry positions |
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Details | One half of the 20S:PA26 complex forms the asymmetric unit. A crystallographic 2-fold operator runs parallel to the 2-fold symmetry axis of the full protein complex. |
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Components
-Protein , 3 types, 21 molecules ABCDEFGHIJKLMNOPQRSTU
#1: Protein | Mass: 25829.447 Da / Num. of mol.: 7 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, 1687 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](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: 2.77 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: PEG 1000, sodium phosphate citrate, LiSO4, imidazole, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-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: 2.3→100 Å / Num. all: 257676 / Num. obs: 257676 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 2.3 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1pma Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.972 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.252 / ESU R Free: 0.199 / 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: 45.254 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.355 Å / Total num. of bins used: 20
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