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- EMDB-34023: EM structure of human PA28gamma -

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Basic information

Entry
Database: EMDB / ID: EMD-34023
TitleEM structure of human PA28gamma
Map data
Sample
  • Organelle or cellular component: Proteasome Activator
    • Protein or peptide: Proteasome activator complex subunit 3
Function / homology
Function and homology information


proteasome activator complex / positive regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / 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 / positive regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / 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 / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / 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 / negative regulation of extrinsic apoptotic signaling pathway / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / 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 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / 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 / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / p53 binding / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / Ub-specific processing proteases / cell cycle / apoptotic process / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteasome activator PA28, N-terminal domain / Proteasome activator PA28, N-terminal domain superfamily / Proteasome activator PA28, N-terminal / Proteasome activator PA28 / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator PA28, C-terminal
Similarity search - Domain/homology
Proteasome activator complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsChen D-D / Hao J / Shen C-H / Yun C-H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071207 China
CitationJournal: 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
DepositionAug 6, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34023.png

Downloads & links

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Map

FileDownload / File: emd_34023.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.0608581 - 1.9495462
Average (Standard dev.)0.00041296246 (±0.055771507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34023_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34023_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Proteasome Activator

EntireName: Proteasome Activator
Components
  • Organelle or cellular component: Proteasome Activator
    • Protein or peptide: Proteasome activator complex subunit 3

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Supramolecule #1: Proteasome Activator

SupramoleculeName: Proteasome Activator / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Proteasome activator complex subunit 3

MacromoleculeName: Proteasome activator complex subunit 3 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.432904 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 395286
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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