8TM4

Human pre 13S proteasome assembly intermediate

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-07-28 Released: 2024-10-23 
  • Deposition Author(s): Zhang, H., Zhao, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of human 20S proteasome biogenesis.

Zhang, H.Zhou, C.Mohammad, Z.Zhao, J.

(2024) Nat Commun 15: 8184-8184

  • DOI: https://doi.org/10.1038/s41467-024-52513-0
  • Primary Citation of Related Structures:  
    8TM3, 8TM4, 8TM5, 8TM6

  • PubMed 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 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.


  • Organizational Affiliation

    Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens)
Explore P25787 
Go to UniProtKB:  P25787
PHAROS:  P25787
GTEx:  ENSG00000106588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25787
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens)
Explore P25789 
Go to UniProtKB:  P25789
PHAROS:  P25789
GTEx:  ENSG00000041357 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25789
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14818 (Homo sapiens)
Explore O14818 
Go to UniProtKB:  O14818
PHAROS:  O14818
GTEx:  ENSG00000101182 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14818
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens)
Explore P28066 
Go to UniProtKB:  P28066
PHAROS:  P28066
GTEx:  ENSG00000143106 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28066
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens)
Explore P25786 
Go to UniProtKB:  P25786
PHAROS:  P25786
GTEx:  ENSG00000129084 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25786
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens)
Explore P25788 
Go to UniProtKB:  P25788
PHAROS:  P25788
GTEx:  ENSG00000100567 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25788
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens)
Explore P60900 
Go to UniProtKB:  P60900
PHAROS:  P60900
GTEx:  ENSG00000100902 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60900
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7277Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens)
Explore Q99436 
Go to UniProtKB:  Q99436
PHAROS:  Q99436
GTEx:  ENSG00000136930 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99436
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49720 (Homo sapiens)
Explore P49720 
Go to UniProtKB:  P49720
PHAROS:  P49720
GTEx:  ENSG00000277791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49720
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49721 (Homo sapiens)
Explore P49721 
Go to UniProtKB:  P49721
PHAROS:  P49721
GTEx:  ENSG00000126067 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49721
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome assembly chaperone 1K [auth c]288Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O95456 (Homo sapiens)
Explore O95456 
Go to UniProtKB:  O95456
PHAROS:  O95456
GTEx:  ENSG00000183527 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95456
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome assembly chaperone 2L [auth d]264Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q969U7 (Homo sapiens)
Explore Q969U7 
Go to UniProtKB:  Q969U7
PHAROS:  Q969U7
GTEx:  ENSG00000128789 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ969U7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome maturation proteinM [auth e]141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y244 (Homo sapiens)
Explore Q9Y244 
Go to UniProtKB:  Q9Y244
PHAROS:  Q9Y244
GTEx:  ENSG00000132963 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y244
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM147487
National Institutes of Health/Office of the DirectorUnited StatesOD026926
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA030199

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection