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Yorodumi- PDB-4gk7: yeast 20S proteasome in complex with the Syringolin-Glidobactin c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gk7 | |||||||||
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Title | yeast 20S proteasome in complex with the Syringolin-Glidobactin chimera | |||||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / proteasome / cancer / protein degradation / inhibition / natural product derivative / NTN-hydrolase / hydrolase-hydrolase inhibitor complex / 12-membered dipeptide-macrolactam | |||||||||
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 / Ub-specific processing proteases / threonine-type endopeptidase activity / 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 | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Groll, M. / Stein, M.L. / Bachmann, A. | |||||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Activity enhancement of the synthetic syrbactin proteasome inhibitor hybrid and biological evaluation in tumor cells. Authors: Archer, C.R. / Groll, M. / Stein, M.L. / Schellenberg, B. / Clerc, J. / Kaiser, M. / Kondratyuk, T.P. / Pezzuto, J.M. / Dudler, R. / Bachmann, A.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gk7.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4gk7.ent.gz | 1016.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/4gk7 ftp://data.pdbj.org/pub/pdb/validation_reports/gk/4gk7 | HTTPS FTP |
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-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 component ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZMaNb
#1: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P23639, proteasome endopeptidase complex #2: Protein | Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P23638, proteasome endopeptidase complex #3: Protein | Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P40303, proteasome endopeptidase complex #4: Protein | Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P32379, proteasome endopeptidase complex #5: Protein | Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P40302, proteasome endopeptidase complex #6: Protein | Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P21242, proteasome endopeptidase complex #7: Protein | Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P21243, proteasome endopeptidase complex #8: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P25451, proteasome endopeptidase complex #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P22141, proteasome endopeptidase complex #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c 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) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P23724, proteasome endopeptidase complex #13: Protein | Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P30657, proteasome endopeptidase complex #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P38624, proteasome endopeptidase complex |
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-Protein/peptide / Non-polymers , 2 types, 1339 molecules 123456
#15: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 550.731 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: (2E,4E)-N-[(2R,3S)-1-{[(5S,8S,9E)-2,7-dioxo-5-(propan-2-yl)-1,6-diazacyclododec-9-en-8-yl]amino}-3-hydroxy-1-oxobutan-2-yl]dodeca-2,4-dienamide #16: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE UNBOUND FORM OF SYLA-GLBA HYBRID MOLECULE HAS A DOUBLE BOND BETWEEN CB AND CG ATOM GROUPS OF ...THE UNBOUND FORM OF SYLA-GLBA HYBRID MOLECULE HAS A DOUBLE BOND BETWEEN CB AND CG ATOM GROUPS OF 0JT COMPONENT. FOLLOWING THE NUCLEOPHIL |
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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: 3.84 Å3/Da / Density % sol: 67.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1M MES, 20mM MgAc2; 12% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2011 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. all: 261503 / Num. obs: 255488 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1RYP Resolution: 2.8→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 6483167.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.5033 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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