+Open data
-Basic information
Entry | Database: PDB / ID: 4g4s | ||||||
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Title | Structure of Proteasome-Pba1-Pba2 Complex | ||||||
Components |
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Keywords | HYDROLASE/CHAPERONE / Alpha Beta / Ntn-hydrolase / Peptide binding / HYDROLASE-CHAPERONE complex | ||||||
Function / homology | Function and homology information 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 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 / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Kish-Trier, E. / Robinson, H. / Stadtmueller, B.M. / Hill, C.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structure of a Proteasome Pba1-Pba2 Complex: IMPLICATIONS FOR PROTEASOME ASSEMBLY, ACTIVATION, AND BIOLOGICAL FUNCTION. Authors: Stadtmueller, B.M. / Kish-Trier, E. / Ferrell, K. / Petersen, C.N. / Robinson, H. / Myszka, D.G. / Eckert, D.M. / Formosa, T. / Hill, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g4s.cif.gz | 718.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g4s.ent.gz | 588.7 KB | Display | PDB format |
PDBx/mmJSON format | 4g4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/4g4s ftp://data.pdbj.org/pub/pdb/validation_reports/g4/4g4s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-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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-Components
-Proteasome component ... , 14 types, 14 molecules ABCDEFGHIJKLMN
#1: Protein | Mass: 28033.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SCL1, PRC2, PRS2, YGL011C / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21243, proteasome endopeptidase complex |
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#2: Protein | Mass: 27191.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE8, PRS4, YML092C / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23639, proteasome endopeptidase complex |
#3: Protein | Mass: 28748.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE9, PRS5, YGR135W / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23638, proteasome endopeptidase complex |
#4: Protein | Mass: 28478.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE6, YOL038W / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P40303, proteasome endopeptidase complex |
#5: Protein | Mass: 28675.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PUP2, DOA5, YGR253C, G9155 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P32379, proteasome endopeptidase complex |
#6: Protein | Mass: 25660.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE5, YMR314W, YM9924.06 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P40302, proteasome endopeptidase complex |
#7: Protein | Mass: 31575.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE10, PRC1, PRS1, YOR362C, O6650 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21242, proteasome endopeptidase complex |
#8: Protein | Mass: 21517.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE3, YJL001W, J1407 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P38624, proteasome endopeptidase complex |
#9: Protein | Mass: 25114.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PUP1, YOR157C / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P25043, proteasome endopeptidase complex |
#10: Protein | Mass: 22627.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PUP3, YER094C / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P25451, proteasome endopeptidase complex |
#11: Protein | Mass: 22545.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE1, YER012W / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P22141, proteasome endopeptidase complex |
#12: Protein | Mass: 23325.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE2, DOA3, PRG1, YPR103W, P8283.10 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P30656, proteasome endopeptidase complex |
#13: Protein | Mass: 24883.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE7, PRS3, PTS1, YBL041W, YBL0407 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P23724, proteasome endopeptidase complex |
#14: Protein | Mass: 25945.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRE4, YFR050C / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P30657, proteasome endopeptidase complex |
-Protein , 2 types, 2 molecules OP
#15: Protein | Mass: 30718.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PBA1, POC1, YLR199C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05778 |
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#16: Protein | Mass: 30917.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: ADD66, PBA2, POC2, YKL206C / Production host: Escherichia coli (E. coli) / References: UniProt: P36040 |
-Non-polymers , 3 types, 855 molecules
#17: Chemical | ChemComp-MG / #18: Chemical | ChemComp-LDZ / | #19: Water | ChemComp-HOH / | |
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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: 2.76 Å3/Da / Density % sol: 55.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium citrate, 18-20% PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→30 Å / Num. all: 162817 / Num. obs: 162817 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→29.778 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 23.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→29.778 Å
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Refine LS restraints |
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LS refinement shell |
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