+Open data
-Basic information
Entry | Database: PDB / ID: 5nif | |||||||||
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Title | Yeast 20S proteasome in complex with Blm-pep activator | |||||||||
Components |
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Keywords | HYDROLASE / 20S proteasome / low-molecular mass activators / allosteric regulation | |||||||||
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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Witkowska, J. / Grudnik, P. / Golik, P. / Dubin, G. / Jankowska, E. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Crystal structure of a low molecular weight activator Blm-pep with yeast 20S proteasome - insights into the enzyme activation mechanism. Authors: Witkowska, J. / Gizynska, M. / Grudnik, P. / Golik, P. / Karpowicz, P. / Giedon, A. / Dubin, G. / Jankowska, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nif.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5nif.ent.gz | 981 KB | Display | PDB format |
PDBx/mmJSON format | 5nif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nif_validation.pdf.gz | 670.6 KB | Display | wwPDB validaton report |
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Full document | 5nif_full_validation.pdf.gz | 793.9 KB | Display | |
Data in XML | 5nif_validation.xml.gz | 215.4 KB | Display | |
Data in CIF | 5nif_validation.cif.gz | 293.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/5nif ftp://data.pdbj.org/pub/pdb/validation_reports/ni/5nif | HTTPS FTP |
-Related structure data
Related structure data | 1rypS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESFT
#1: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P21243, proteasome endopeptidase complex #2: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P23639, proteasome endopeptidase complex #3: Protein | Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P23638, proteasome endopeptidase complex #4: Protein | Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P40303, proteasome endopeptidase complex #5: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32379, proteasome endopeptidase complex #6: Protein | Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P40302, proteasome endopeptidase complex |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZM1N2
#8: Protein | Mass: 23573.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P38624, proteasome endopeptidase complex #9: Protein | Mass: 28299.889 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P25043, proteasome endopeptidase complex #10: Protein | Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P25451, proteasome endopeptidase complex #11: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P22141, proteasome endopeptidase complex #12: Protein | Mass: 31670.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P30656, proteasome endopeptidase complex #13: Protein | Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P23724, proteasome endopeptidase complex #14: Protein | Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P30657, proteasome endopeptidase complex |
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-Protein / Protein/peptide , 2 types, 4 molecules GU34
#15: Protein/peptide | Mass: 1773.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) #7: Protein | Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P21242, proteasome endopeptidase complex |
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-Non-polymers , 5 types, 109 molecules
#16: Chemical | ChemComp-CL / #17: Chemical | ChemComp-MG / #18: Chemical | ChemComp-EDO / #19: Chemical | ChemComp-GOL / #20: 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: 3.49 Å3/Da / Density % sol: 64.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 35mM magnesium acetate, 13% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 3→50.01 Å / Num. obs: 210084 / % possible obs: 99.93 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3→3.107 Å / Num. unique obs: 20926 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RYP Resolution: 3→50.01 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→50.01 Å
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Refine LS restraints |
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LS refinement shell |
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