+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15767 | |||||||||
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Title | Bovine 20S proteasome, untreated | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Keywords | 20S proteasome / Degradation / Proteolysis / HYDROLASE | |||||||||
Function / homology | Function and homology information Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL ...Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / NIK-->noncanonical NF-kB signaling / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Interleukin-1 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of beta-catenin by the destruction complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / UCH proteinases / ABC-family proteins mediated transport / Ub-specific processing proteases / Downstream TCR signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / proteasome core complex / Neutrophil degranulation / immune system process / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / ciliary basal body / proteolysis involved in protein catabolic process / lipopolysaccharide binding / P-body / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / postsynapse / centrosome / synapse / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Szenkier N / Arie M / Matzov D / Sertchook R / Carmeli R / Cascio P / Stanhill A / Shalev Benami M / Navon A | |||||||||
Funding support | Israel, 1 items
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Citation | Journal: To be published Title: Bovine 20S proteasome, untreated Authors: Szenkier N / Arie M / Matzov D / Sertchook R / Carmeli R / Cascio P / Stanhill A / Shalev Benami M / Navon A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15767.map.gz | 285.4 MB | EMDB map data format | |
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Header (meta data) | emd-15767-v30.xml emd-15767.xml | 29.3 KB 29.3 KB | Display Display | EMDB header |
Images | emd_15767.png | 66.6 KB | ||
Filedesc metadata | emd-15767.cif.gz | 7.5 KB | ||
Others | emd_15767_additional_1.map.gz emd_15767_half_map_1.map.gz emd_15767_half_map_2.map.gz | 156.8 MB 279.9 MB 279.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15767 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15767 | HTTPS FTP |
-Validation report
Summary document | emd_15767_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_15767_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_15767_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | emd_15767_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15767 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15767 | HTTPS FTP |
-Related structure data
Related structure data | 8azkMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15767.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_15767_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_15767_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_15767_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Untreated 20S proteasome
+Supramolecule #1: Untreated 20S proteasome
+Macromolecule #1: Proteasome subunit beta type-3
+Macromolecule #2: Proteasome subunit alpha type-6
+Macromolecule #3: Proteasome subunit alpha type-2
+Macromolecule #4: Proteasome subunit alpha type-4
+Macromolecule #5: Proteasome subunit alpha type-7
+Macromolecule #6: Proteasome subunit alpha type-5
+Macromolecule #7: Proteasome subunit alpha type-1
+Macromolecule #8: Proteasome subunit alpha type-3
+Macromolecule #9: Proteasome subunit beta type-6
+Macromolecule #10: Proteasome subunit beta type-7
+Macromolecule #11: Proteasome subunit beta type-2
+Macromolecule #12: Proteasome subunit beta type-5
+Macromolecule #13: Proteasome subunit beta type-1
+Macromolecule #14: Proteasome subunit beta type-4
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE / Details: Ab initio reconstruction |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 346962 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |