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- PDB-8tm3: Human proteasome alpha ring assembly intermediate -

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Basic information

Entry
Database: PDB / ID: 8tm3
TitleHuman proteasome alpha ring assembly intermediate
Components
  • (Proteasome assembly chaperone ...) x 4
  • (Proteasome subunit alpha type- ...) x 7
KeywordsHYDROLASE / proteasome / proteasome assembly / PAC3 / PAC4
Function / homology
Function and homology information


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 ...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 assembly / chaperone-mediated protein complex assembly / proteasome core complex, alpha-subunit complex / proteasome complex / proteolysis involved in protein catabolic process / 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 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Degradation of AXIN / Hh mutants are degraded by ERAD / negative regulation of inflammatory response to antigenic stimulus / P-body / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / 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 / response to virus / 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 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / positive regulation of NF-kappaB transcription factor activity / Regulation of RUNX2 expression and activity / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / regulation of inflammatory response / secretory granule lumen / endopeptidase activity / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Ub-specific processing proteases / cilium / ribosome / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / protein-containing complex / mitochondrion
Similarity search - Function
Proteasome assembly chaperone 4 / Proteasome assembly chaperone 4 / Proteasome assembly chaperone 3 / Proteasome assembly chaperone 3 / : / Proteasome assembly chaperone 1 / Proteasome assembly chaperone 4 / Proteasome assembly chaperone 2, eukaryotic / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily ...Proteasome assembly chaperone 4 / Proteasome assembly chaperone 4 / Proteasome assembly chaperone 3 / Proteasome assembly chaperone 3 / : / Proteasome assembly chaperone 1 / Proteasome assembly chaperone 4 / Proteasome assembly chaperone 2, eukaryotic / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Proteasome subunit alpha 1 / Proteasome subunit alpha6 / Proteasome subunit alpha5 / 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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit alpha type-7 / Proteasome assembly chaperone 1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit alpha type-6 / Proteasome assembly chaperone 4 / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhang, H. / Zhao, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147487 United States
National Institutes of Health/Office of the DirectorOD026926 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA030199 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis of human 20S proteasome biogenesis.
Authors: Hanxiao Zhang / Chenyu Zhou / Zarith Mohammad / Jianhua Zhao /
Abstract: New proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the ...New proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the function of the five chaperones PAC1-4 and POMP. Here, to understand how these chaperones facilitate proteasome assembly, we tagged the endogenous chaperones using CRISPR/Cas gene editing and examined the chaperone-bound complexes by cryo-EM. We observe an early α-ring intermediate subcomplex that is stabilized by PAC1-4, which transitions to β-ring assembly upon dissociation of PAC3/PAC4 and rearrangement of the PAC1 N-terminal tail. Completion of the β-ring and dimerization of half-proteasomes repositions critical lysine K33 to trigger cleavage of the β pro-peptides, leading to the concerted dissociation of POMP and PAC1/PAC2 to yield mature 20S proteasomes. This study reveals structural insights into critical points along the assembly pathway of the human proteasome and provides a molecular blueprint for 20S biogenesis.
History
DepositionJul 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 23, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 23, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Oct 23, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 23, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 23, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 23, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 23, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 23, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 23, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
c: Proteasome assembly chaperone 1
d: Proteasome assembly chaperone 2
i: Proteasome assembly chaperone 3
j: Proteasome assembly chaperone 4


Theoretical massNumber of molelcules
Total (without water)284,54011
Polymers284,54011
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 alpha type- ... , 7 types, 7 molecules ABCDEFG

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F
References: UniProt: P25787, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F
References: UniProt: P25789, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27929.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F
References: UniProt: O14818, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F
References: UniProt: P28066, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29595.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F
References: UniProt: P25786, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F
References: UniProt: P25788, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-6 / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27432.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F
References: UniProt: P60900, proteasome endopeptidase complex

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Proteasome assembly chaperone ... , 4 types, 4 molecules cdij

#8: Protein Proteasome assembly chaperone 1 / PAC-1 / Chromosome 21 leucine-rich protein / C21-LRP / Down syndrome critical region protein 2


Mass: 32891.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F / References: UniProt: O95456
#9: Protein Proteasome assembly chaperone 2 / PAC-2 / Hepatocellular carcinoma-susceptibility protein 3 / Tumor necrosis factor superfamily ...PAC-2 / Hepatocellular carcinoma-susceptibility protein 3 / Tumor necrosis factor superfamily member 5-induced protein 1


Mass: 29423.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F / References: UniProt: Q969U7
#10: Protein Proteasome assembly chaperone 3 / PAC-3 / hPAC3


Mass: 13118.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F / References: UniProt: Q9BT73
#11: Protein Proteasome assembly chaperone 4 / PAC-4 / hPAC4


Mass: 13789.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293F / References: UniProt: Q5JS54

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Details

Has protein modificationY

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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 alpha ring assembly intermediate / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Cell: Expi293F / Cellular location: cytoplasm
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2150 mMsodium chlorideNaCl1
31 mMDTT1
SpecimenConc.: 0.5 mg/ml / Embedding 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 1700 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111057 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317894
ELECTRON MICROSCOPYf_angle_d0.51924355
ELECTRON MICROSCOPYf_dihedral_angle_d3.792546
ELECTRON MICROSCOPYf_chiral_restr0.0392881
ELECTRON MICROSCOPYf_plane_restr0.0053113

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