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- PDB-4ltc: Crystal structure of yeast 20S proteasome in complex with enone c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ltc | ||||||
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Title | Crystal structure of yeast 20S proteasome in complex with enone carmaphycin analogue 6 | ||||||
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![]() | Hydrolase/Hydrolase Inhibitor / proteasome / inhibitor / carmaphycin / epoxyketone / vinylketone / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stein, M. / Trivella, D.B.B. / Groll, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.4 MB | Display | ![]() |
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PDB format | ![]() | 2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 233 KB | Display | |
Data in CIF | ![]() | 328.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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:
NCS domain segments:
NCS ensembles :
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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) ![]() ![]() References: UniProt: P23639, proteasome endopeptidase complex #2: Protein | Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P23638, proteasome endopeptidase complex #3: Protein | Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P40303, proteasome endopeptidase complex #4: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P32379, proteasome endopeptidase complex #5: Protein | Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P40302, proteasome endopeptidase complex #7: Protein | Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P21243, proteasome endopeptidase complex |
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-Protein , 1 types, 2 molecules FT
#6: Protein | Mass: 31443.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P21242, proteasome endopeptidase complex |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#8: Protein | Mass: 25114.459 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() References: UniProt: P38624, proteasome endopeptidase complex |
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-Non-polymers , 2 types, 2609 molecules ![](data/chem/img/EC6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#15: Chemical | ![]() Details: Originated from (S)-N1-((S,Z)-2,6-dimethyl-5-oxooct-6-en-4-yl)-2-((S)-2-hexanamido-3-methylbutanamido)-N5,N5-dimethylpentanediamide that reacts with N-terminal Thr of the protein, opening ...Details: Originated from (S)-N1-((S,Z)-2,6-dimethyl-5-oxooct-6-en-4-yl)-2-((S)-2-hexanamido-3-methylbutanamido)-N5,N5-dimethylpentanediamide that reacts with N-terminal Thr of the protein, opening double bonds of the original compound and making two covalent linkages with the amino group and side chain hydroxyl of the Thr. The PRD represents the bound form. References: N-HEXANOYL-L-VALYL-N~1~-[(4S,5S,6R)-5-HYDROXY-2,6-DIMETHYLOCTAN-4-YL]-N~5~,N~5~-DIMETHYL-L-GLUTAMAMIDE #16: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.83 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / 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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | Highest resolution: 2.5 Å / Num. obs: 354256 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 55.34 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.34 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 153.79 Å2 / Biso mean: 57.9261 Å2 / Biso min: 16.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 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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