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- PDB-7yqc: EM structure of human PA28gamma -

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Basic information

Entry
Database: PDB / ID: 7yqc
TitleEM structure of human PA28gamma
ComponentsProteasome activator complex subunit 3
KeywordsPROTEIN TRANSPORT / proteasome activator gamma / PA28gamma / PSME3
Function / homology
Function and homology information


proteasome activator complex / Proteasome assembly / 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 / negative regulation of extrinsic apoptotic signaling pathway / p53 binding / ciliary basal body ...proteasome activator complex / Proteasome assembly / 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 / negative regulation of extrinsic apoptotic signaling pathway / p53 binding / ciliary basal body / cilium / apoptotic process / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsChen, D.-D. / Hao, J. / Shen, C.-H. / Yun, C.-H.
Funding support China, 1items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome activator complex subunit 3
B: Proteasome activator complex subunit 3
C: Proteasome activator complex subunit 3
D: Proteasome activator complex subunit 3
E: Proteasome activator complex subunit 3
F: Proteasome activator complex subunit 3
G: Proteasome activator complex subunit 3


Theoretical massNumber of molelcules
Total (without water)206,0307
Polymers206,0307
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Proteasome activator complex subunit 3 / 11S regulator complex subunit gamma / REG-gamma / Activator of multicatalytic protease subunit 3 / ...11S regulator complex subunit gamma / REG-gamma / Activator of multicatalytic protease subunit 3 / Ki nuclear autoantigen / Proteasome activator 28 subunit gamma / PA28g / PA28gamma


Mass: 29432.904 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSME3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61289

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Proteasome Activator / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 395286 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0211550
ELECTRON MICROSCOPYf_angle_d2.25715568
ELECTRON MICROSCOPYf_dihedral_angle_d18.9814529
ELECTRON MICROSCOPYf_chiral_restr0.161848
ELECTRON MICROSCOPYf_plane_restr0.011953

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