+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34023 | |||||||||
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Title | EM structure of human PA28gamma | |||||||||
Map data | ||||||||||
Sample |
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Keywords | proteasome activator gamma / PA28gamma / PSME3 / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information proteasome activator complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / regulation of proteasomal protein catabolic process / MDM2/MDM4 family protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation ...proteasome activator complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / regulation of proteasomal protein catabolic process / MDM2/MDM4 family protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / negative regulation of extrinsic apoptotic signaling pathway / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / 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 / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Interleukin-1 signaling / Regulation of PTEN stability and activity / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / p53 binding / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / Ub-specific processing proteases / apoptotic process / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.82 Å | |||||||||
Authors | Chen D-D / Hao J / Shen C-H / Yun C-H | |||||||||
Funding support | China, 1 items
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Citation | Journal: Int J Biol Macromol / Year: 2022 Title: Atomic resolution Cryo-EM structure of human proteasome activator PA28γ. Authors: Dan-Dan Chen / Jia Hao / Chao-Hui Shen / Xian-Ming Deng / Cai-Hong Yun / Abstract: The PA28 family proteasome activators play important roles in regulating proteasome activities. Though the three paralogs (PA28α, PA28β, and PA28γ) are similar in terms of primary sequence, they ...The PA28 family proteasome activators play important roles in regulating proteasome activities. Though the three paralogs (PA28α, PA28β, and PA28γ) are similar in terms of primary sequence, they show significant differences in expression pattern, cellular localization and most importantly, biological functions. While PA28αβ is responsible for promoting peptidase activity of proteasome to facilitate MHC-I antigen processing, but unable to promote protein degradation, PA28γ is well-known to not only promote peptidase activity but also proteolytic activity of proteasome. However, why this paralog has the unique function remains elusive. Previous structural studies have mainly focused on mammalian PA28α, PA28β and PA28αβ heptamers, while structural studies on mammalian PA28γ of atomic resolution are still absent to date. In the present work, we determined the Cryo-EM structure of the human PA28γ heptamer at atomic resolution, revealing interesting unique structural features that may hint our understanding the functional mechanisms of this proteasome activator. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34023.map.gz | 49.6 MB | EMDB map data format | |
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Header (meta data) | emd-34023-v30.xml emd-34023.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_34023.png | 113.9 KB | ||
Filedesc metadata | emd-34023.cif.gz | 4.9 KB | ||
Others | emd_34023_half_map_1.map.gz emd_34023_half_map_2.map.gz | 45.8 MB 45.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34023 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34023 | HTTPS FTP |
-Validation report
Summary document | emd_34023_validation.pdf.gz | 785.4 KB | Display | EMDB validaton report |
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Full document | emd_34023_full_validation.pdf.gz | 785 KB | Display | |
Data in XML | emd_34023_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | emd_34023_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34023 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34023 | HTTPS FTP |
-Related structure data
Related structure data | 7yqcMC 7yqdC 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_34023.map.gz / Format: CCP4 / Size: 52.7 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: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34023_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34023_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Proteasome Activator
Entire | Name: Proteasome Activator |
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Components |
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-Supramolecule #1: Proteasome Activator
Supramolecule | Name: Proteasome Activator / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Proteasome activator complex subunit 3
Macromolecule | Name: Proteasome activator complex subunit 3 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 29.432904 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASLLKVDQE VKLKVDSFRE RITSEAEDLV ANFFPKKLLE LDSFLKEPIL NIHDLTQIHS DMNLPVPDPI LLTNSHDGLD GPTYKKRRL DECEEAFQGT KVFVMPNGML KSNQQLVDII EKVKPEIRLL IEKCNTVKMW VQLLIPRIED GNNFGVSIQE E TVAELRTV ...String: MASLLKVDQE VKLKVDSFRE RITSEAEDLV ANFFPKKLLE LDSFLKEPIL NIHDLTQIHS DMNLPVPDPI LLTNSHDGLD GPTYKKRRL DECEEAFQGT KVFVMPNGML KSNQQLVDII EKVKPEIRLL IEKCNTVKMW VQLLIPRIED GNNFGVSIQE E TVAELRTV ESEAASYLDQ ISRYYITRAK LASKIAKYPH VEDYARTVTE IDEKEYISLR LIISELRNQY VTLHDMILKN IE KIKRPRS SNAETLY UniProtKB: Proteasome activator complex subunit 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 395286 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |