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- PDB-9qbw: Yeast 20S proteasome mutant: beta5_G128V (b5-propeptide in trans)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9qbw | ||||||
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Title | Yeast 20S proteasome mutant: beta5_G128V (b5-propeptide in trans) in complex with Carfilzomib | ||||||
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![]() | HYDROLASE / Proteasome / Proteasome Associated Autoinflammatory Syndromes / Mutation / Assembly / Maturation | ||||||
Function / homology | ![]() proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, E.M. / Heinemeyer, W. / Groll, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Proteasome-associated autoinflammatory syndromes: The impact of mutations in proteasome subunits on particle assembly, structure, and activity Authors: Huber, E.M. / Heinemeyer, W. / 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 | ![]() | 2.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 662.3 KB | Display | ![]() |
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Full document | ![]() | 723.5 KB | Display | |
Data in XML | ![]() | 229 KB | Display | |
Data in CIF | ![]() | 302.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9qafC ![]() 9qaiC ![]() 9qb1C ![]() 9qb4C ![]() 9qbeC ![]() 9qbiC ![]() 9qboC ![]() 9qbyC ![]() 9qc9C ![]() 9qcfC ![]() 9qckC ![]() 9qd2C ![]() 9qdfC ![]() 9qdsC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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:
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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) ![]() ![]() #2: Protein | Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#8: Protein | Mass: 25013.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 23266.225 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PRE2, DOA3, PRG1, YPR103W, P8283.10 / Production host: ![]() ![]() References: UniProt: P30656, proteasome endopeptidase complex #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 21416.080 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P38624, proteasome endopeptidase complex |
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-Protein / Protein/peptide , 2 types, 8 molecules FTfghijk
#15: Protein/peptide | Mass: 857.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #6: Protein | Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 195 molecules 










#16: Chemical | #17: Chemical | ChemComp-CL / #18: Chemical | ChemComp-MES / #19: Chemical | #20: Chemical | ChemComp-SO4 / | #21: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.34 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2015 |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 232521 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 22802 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 65.927 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→15 Å
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Refine LS restraints |
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