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Yorodumi- PDB-4hrd: Crystal structure of yeast 20S proteasome in complex with the nat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hrd | ||||||
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Title | Crystal structure of yeast 20S proteasome in complex with the natural product carmaphycin A | ||||||
Components | (Proteasome component ...) x 14 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / proteasome / inhibitor / carmaphycin / epoxyketone / vinylketone / HYDROLASE-HYDROLASE INHIBITOR 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 / 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) Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Trivella, D.B.B. / Stein, M. / Groll, M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2014 Title: Enzyme inhibition by hydroamination: design and mechanism of a hybrid carmaphycin-syringolin enone proteasome inhibitor. Authors: Trivella, D.B. / Pereira, A.R. / Stein, M.L. / Kasai, Y. / Byrum, T. / Valeriote, F.A. / Tantillo, D.J. / Groll, M. / Gerwick, W.H. / Moore, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hrd.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4hrd.ent.gz | 2.1 MB | Display | PDB format |
PDBx/mmJSON format | 4hrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hrd_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 4hrd_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4hrd_validation.xml.gz | 215.2 KB | Display | |
Data in CIF | 4hrd_validation.cif.gz | 296.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/4hrd ftp://data.pdbj.org/pub/pdb/validation_reports/hr/4hrd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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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 S288c (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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-Non-polymers , 2 types, 960 molecules
#15: Chemical | ChemComp-OV1 / Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 519.738 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C25H49N3O6S / Details: Carmaphycin A, bound form References: N-[(2S)-1-({(2S)-1-{[(2R,3S,4S)-1,3-DIHYDROXY-2,6-DIMETHYLHEPTAN-4-YL]AMINO}-4-[(R)-METHYLSULFINYL]-1-OXOBUTAN-2-YL}AMINO)-3-METHYL-1-OXOBUTAN-2-YL]HEXANAMIDE #16: 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: 3.83 Å3/Da / Density % sol: 67.92 % |
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Crystal grow | Temperature: 297 K / pH: 7.5 Details: 30 mM of magnesium acetate, 100 mM of MES (pH 7.2) and 12% of MPD, vapor diffusion, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2012 |
Radiation | Monochromator: DOUBLE MULTILAYER 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→49.59 Å / Num. obs: 254447 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.13 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.94 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.61 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.59 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 31.548 / SU ML: 0.268 / SU R Cruickshank DPI: 0.6683 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.668 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→49.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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