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- PDB-9x4e: Structure of the old Killifish Proteasome -

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Basic information

Entry
Database: PDB / ID: 9x4e
TitleStructure of the old Killifish Proteasome
Components(Proteasome subunit ...) x 14
KeywordsHYDROLASE / Proteasome / Nothobranchius furzeri / aging / skeletal muscle
Function / homology
Function and homology information


proteasome core complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit ...Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta ...Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit alpha type
Similarity search - Component
Biological speciesNothobranchius furzeri (turquoise killifish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsKim, J. / Song, J.J. / Kim, Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2024-00333346 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00266300 Korea, Republic Of
CitationJournal: To Be Published
Title: Ribosome remodels in age-dependent manner
Authors: Kim, J. / Hyeon, D.Y. / Lee, S. / Ryu, B.H. / Gwak, N. / Choi, Y. / Vu, H.M. / Huh, S. / Kim, S. / Myung, K. / Dieterich, C. / Valenzano, D.R. / Kim, M.S. / Hwang, D. / Song, J.J. / Kim, Y.
History
DepositionOct 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type
B: Proteasome subunit alpha type
C: Proteasome subunit alpha type
D: Proteasome subunit alpha type
E: Proteasome subunit alpha type
F: Proteasome subunit alpha type
G: Proteasome subunit alpha type
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit 5
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome subunit alpha type
P: Proteasome subunit alpha type
Q: Proteasome subunit alpha type
R: Proteasome subunit alpha type
S: Proteasome subunit alpha type
T: Proteasome subunit alpha type
U: Proteasome subunit alpha type
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit 5
a: Proteasome subunit beta
b: Proteasome subunit beta


Theoretical massNumber of molelcules
Total (without water)766,89628
Polymers766,89628
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Proteasome subunit ... , 14 types, 28 molecules AOBPCQDRESFTGUHXIWJVKZLYMaNb

#1: Protein Proteasome subunit alpha type


Mass: 25900.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZN72
#2: Protein Proteasome subunit alpha type


Mass: 29405.709 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8B0E3
#3: Protein Proteasome subunit alpha type


Mass: 28143.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8V7S3
#4: Protein Proteasome subunit alpha type


Mass: 26445.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8V3Y9
#5: Protein Proteasome subunit alpha type


Mass: 29380.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UYX9
#6: Protein Proteasome subunit alpha type


Mass: 28428.021 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZU17
#7: Protein Proteasome subunit alpha type


Mass: 27471.342 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8U241
#8: Protein Proteasome subunit beta


Mass: 25022.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8A9L4
#9: Protein Proteasome subunit beta


Mass: 23050.857 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8ANK7
#10: Protein Proteasome subunit beta


Mass: 29726.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8TWU4
#11: Protein Proteasome subunit 5


Mass: 32160.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Sequence refers to XP_054589013.1
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle
#12: Protein Proteasome subunit beta


Mass: 23931.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A7ZAT0
#13: Protein Proteasome subunit beta


Mass: 28307.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8AVF5
#14: Protein Proteasome subunit beta


Mass: 26073.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nothobranchius furzeri (turquoise killifish)
Tissue: skeletal muscle / References: UniProt: A0A1A8UKL0

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Details

Has protein modificationN

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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: Structure of the old Killifish Proteasome / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMPotassium ChlorideKCl1
215 mMMagnesium ChlorideMgCl21
320 mMTris-hydrochlorideTris-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 5.87 sec. / Electron dose: 60.23 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 9136
EM imaging opticsEnergyfilter name: GIF Bioquantum / Details: BioQuantum K3 Imaging filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.2.1particle selectiontemplate based picking
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2953254
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121745 / Symmetry type: POINT
RefinementCross valid method: NONE

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