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Yorodumi- EMDB-39334: Cryo-EM structure of human proteasome assembly intermediate preholo-2 -
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Basic information
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| Title | Cryo-EM structure of human proteasome assembly intermediate preholo-2 | |||||||||
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Keywords | Protein degradation / Proteasome / 20S proteasome / Assembly / Assembly chapreone / STRUCTURAL PROTEIN | |||||||||
| Function / homology | Function and homology informationcerebellar granule cell precursor proliferation / purine ribonucleoside triphosphate binding / protein folding chaperone complex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / proteasome core complex assembly / Somitogenesis / mitotic spindle assembly checkpoint signaling ...cerebellar granule cell precursor proliferation / purine ribonucleoside triphosphate binding / protein folding chaperone complex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / proteasome core complex assembly / Somitogenesis / mitotic spindle assembly checkpoint signaling / proteasome binding / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / chaperone-mediated protein complex assembly / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteolysis involved in protein catabolic process / proteasome complex / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / negative regulation of inflammatory response to antigenic stimulus / Degradation of AXIN / P-body / Hh mutants are degraded by ERAD / lipopolysaccharide binding / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Regulation of RUNX3 expression and activity / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / response to virus / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / nuclear matrix / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / peptidase activity / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / regulation of inflammatory response / response to oxidative stress / secretory granule lumen / endopeptidase activity / molecular adaptor activity / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / nuclear body / cilium / ciliary basal body / ribosome / cadherin binding / intracellular membrane-bounded organelle / ubiquitin protein ligase binding Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.79 Å | |||||||||
Authors | Han Y / Han Q / Tang Q / Zhang Y / Liu K | |||||||||
| Funding support | China, 2 items
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Citation | Journal: Sci Adv / Year: 2025Title: Molecular basis for the stepwise and faithful maturation of the 20 proteasome. Authors: Yaoyao Han / Qian Han / Qianqian Tang / Yixiao Zhang / Kai Liu / ![]() Abstract: The proteasome degrades most superfluous and damaged proteins, and its decline is associated with many diseases. As the proteolytic unit, the 20 proteasome is assembled from 28 subunits assisted by ...The proteasome degrades most superfluous and damaged proteins, and its decline is associated with many diseases. As the proteolytic unit, the 20 proteasome is assembled from 28 subunits assisted by chaperones PAC1/2/3/4 and POMP; then, it undergoes the maturation process, in which the proteolytic sites are activated and the assembly chaperones are cleared. However, mechanisms governing the maturation remain elusive. Here, we captured endogenous maturation intermediates of human 20 proteasome, which are low abundance and highly dynamic, and determined their structures by cryo-electron microscopy. Through structure-based functional studies, we identified the key switches that remodel and activate the proteolytic sites. Our results also revealed that the POMP degradation is tightly controlled by a dual-checking mechanism, while the α5 subunit senses POMP degradation to induce PAC1/2 release, achieving the full maturation. These findings elucidate mechanisms directing and safeguarding the proteasome maturation and set basis for building proteasomes to counteract the decline of protein degradation in aging and disease. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_39334.map.gz | 48.5 MB | EMDB map data format | |
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| Header (meta data) | emd-39334-v30.xml emd-39334.xml | 32.5 KB 32.5 KB | Display Display | EMDB header |
| Images | emd_39334.png | 133.7 KB | ||
| Filedesc metadata | emd-39334.cif.gz | 8.7 KB | ||
| Others | emd_39334_half_map_1.map.gz emd_39334_half_map_2.map.gz | 67.4 MB 67.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39334 | HTTPS FTP |
-Validation report
| Summary document | emd_39334_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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| Full document | emd_39334_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | emd_39334_validation.xml.gz | 13.5 KB | Display | |
| Data in CIF | emd_39334_validation.cif.gz | 16 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39334 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39334 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8yizMC ![]() 8yixC ![]() 8yiyC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_39334.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_39334_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_39334_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Cryo-EM structure of human proteasome assembly intermediate preholo-2
+Supramolecule #1: Cryo-EM structure of human proteasome assembly intermediate preholo-2
+Macromolecule #1: Proteasome subunit alpha type-2
+Macromolecule #2: Proteasome subunit alpha type-4
+Macromolecule #3: Proteasome subunit alpha type-7
+Macromolecule #4: Proteasome subunit alpha type-5
+Macromolecule #5: Proteasome subunit alpha type-1
+Macromolecule #6: Proteasome subunit alpha type-3
+Macromolecule #7: Proteasome subunit alpha type-6
+Macromolecule #8: Proteasome subunit beta type-7
+Macromolecule #9: Proteasome subunit beta type-3
+Macromolecule #10: Proteasome subunit beta type-2
+Macromolecule #11: Proteasome subunit beta type-5
+Macromolecule #12: Proteasome subunit beta type-1
+Macromolecule #13: Proteasome subunit beta type-4
+Macromolecule #14: Proteasome subunit beta type-6
+Macromolecule #15: Proteasome assembly chaperone 1
+Macromolecule #16: Proteasome assembly chaperone 2
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.9 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TECNAI 12 |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.41 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
China, 2 items
Citation











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Processing
FIELD EMISSION GUN
