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- PDB-5fgi: Yeast 20S proteasome beta1-T1A beta2-T1A double mutant in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fgi | ||||||
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Title | Yeast 20S proteasome beta1-T1A beta2-T1A double mutant in complex with Carfilzomib | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / ![]() ![]() | ||||||
Function / homology | ![]() 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 / proteasome storage granule / endopeptidase activator activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, E.M. / Groll, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome. Authors: Huber, E.M. / Heinemeyer, W. / Li, X. / Arendt, C.S. / Hochstrasser, M. / Groll, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.4 MB | Display | ![]() |
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PDB format | ![]() | 2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5cz4C ![]() 5cz5C ![]() 5cz6C ![]() 5cz7C ![]() 5cz8C ![]() 5cz9C ![]() 5czaC ![]() 5d0sC ![]() 5d0tC ![]() 5d0vC ![]() 5d0wC ![]() 5d0xC ![]() 5d0zC ![]() 5fg7C ![]() 5fg9C ![]() 5fgaC ![]() 5fgdC ![]() 5fgeC ![]() 5fgfC ![]() 5fggC ![]() 5fghC ![]() 5fhsC ![]() 1rypS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
-Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU
#1: Protein | ![]() Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P23639, ![]() #2: Protein | ![]() Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P23638, ![]() #3: Protein | ![]() Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P40303, ![]() #4: Protein | ![]() Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P32379, ![]() #5: Protein | ![]() Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P40302, ![]() #7: Protein | ![]() Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P21243, ![]() |
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-Protein , 1 types, 2 molecules FT
#6: Protein | Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P21242, ![]() |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#8: Protein | ![]() Mass: 26296.705 Da / Num. of mol.: 2 / Mutation: T1A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: P25043, ![]() #9: Protein | ![]() Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P25451, ![]() #10: Protein | ![]() Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P22141, ![]() #11: Protein | ![]() Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P30656, ![]() #12: Protein | ![]() Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P23724, ![]() #13: Protein | ![]() Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P30657, ![]() #14: Protein | ![]() Mass: 23298.277 Da / Num. of mol.: 2 / Mutation: T1A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: P38624, ![]() |
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-Non-polymers , 5 types, 241 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/3BV.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/3BV.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#15: Chemical | ChemComp-MG / #16: Chemical | ChemComp-CL / ![]() #17: Chemical | ![]() ![]() #18: Chemical | ![]() #19: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.52 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH range: 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2014 |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→30 Å / Num. obs: 232107 / % possible obs: 97.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1RYP Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 29.52 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R Free: 0.299 / 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: 65.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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