6TU3

Rat 20S proteasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry.

Vimer, S.Ben-Nissan, G.Morgenstern, D.Kumar-Deshmukh, F.Polkinghorn, C.Quintyn, R.S.Vasil'ev, Y.V.Beckman, J.S.Elad, N.Wysocki, V.H.Sharon, M.

(2020) ACS Cent Sci 6: 573-588

  • DOI: 10.1021/acscentsci.0c00080
  • Primary Citation of Related Structures:  
    6TU3

  • PubMed Abstract: 
  • Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures ...

    Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the Thermoplasma acidophilum archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast ( Saccharomyces cerevisiae ) and mammals (rat - Rattus norvegicus , rabbit - Oryctolagus cuniculus and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.


    Organizational Affiliation

    Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6A, X [auth O]246Rattus norvegicusMutation(s): 0 
Gene Names: Psma6
EC: 3.4.25.1
UniProt
Find proteins for P60901 (Rattus norvegicus)
Explore P60901 
Go to UniProtKB:  P60901
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B, O [auth P]234Rattus norvegicusMutation(s): 0 
Gene Names: Psma2
EC: 3.4.25.1
UniProt
Find proteins for P17220 (Rattus norvegicus)
Explore P17220 
Go to UniProtKB:  P17220
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C, AA [auth Q]261Rattus norvegicusMutation(s): 0 
Gene Names: Psma4
EC: 3.4.25.1
UniProt
Find proteins for P21670 (Rattus norvegicus)
Explore P21670 
Go to UniProtKB:  P21670
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7D, W [auth R]254Rattus norvegicusMutation(s): 0 
Gene Names: Psma7
EC: 3.4.25.1
UniProt
Find proteins for P48004 (Rattus norvegicus)
Explore P48004 
Go to UniProtKB:  P48004
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E, Z [auth S]241Rattus norvegicusMutation(s): 0 
Gene Names: Psma5
EC: 3.4.25.1
UniProt
Find proteins for P34064 (Rattus norvegicus)
Explore P34064 
Go to UniProtKB:  P34064
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1F, P [auth T]263Rattus norvegicusMutation(s): 0 
Gene Names: Psma1
EC: 3.4.25.1
UniProt
Find proteins for P18420 (Rattus norvegicus)
Explore P18420 
Go to UniProtKB:  P18420
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3G, Y [auth U]255Rattus norvegicusMutation(s): 0 
Gene Names: Psma3
EC: 3.4.25.1
UniProt
Find proteins for P18422 (Rattus norvegicus)
Explore P18422 
Go to UniProtKB:  P18422
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6H, BA [auth V]238Rattus norvegicusMutation(s): 0 
Gene Names: Psmb6Psmb6l
EC: 3.4.25.1
UniProt
Find proteins for P28073 (Rattus norvegicus)
Explore P28073 
Go to UniProtKB:  P28073
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7I, V [auth W]277Rattus norvegicusMutation(s): 0 
Gene Names: Psmb7
EC: 3.4.25.1
UniProt
Find proteins for Q9JHW0 (Rattus norvegicus)
Explore Q9JHW0 
Go to UniProtKB:  Q9JHW0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3J, Q [auth X]205Rattus norvegicusMutation(s): 0 
Gene Names: Psmb3
EC: 3.4.25.1
UniProt
Find proteins for P40112 (Rattus norvegicus)
Explore P40112 
Go to UniProtKB:  P40112
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2K, R [auth Y]201Rattus norvegicusMutation(s): 0 
Gene Names: Psmb2
EC: 3.4.25.1
UniProt
Find proteins for P40307 (Rattus norvegicus)
Explore P40307 
Go to UniProtKB:  P40307
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5L, S [auth Z]263Rattus norvegicusMutation(s): 0 
Gene Names: Psmb5
EC: 3.4.25.1
UniProt
Find proteins for P28075 (Rattus norvegicus)
Explore P28075 
Go to UniProtKB:  P28075
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1M, T [auth a]240Rattus norvegicusMutation(s): 0 
Gene Names: Psmb1
EC: 3.4.25.1
UniProt
Find proteins for P18421 (Rattus norvegicus)
Explore P18421 
Go to UniProtKB:  P18421
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4N, U [auth b]263Rattus norvegicusMutation(s): 0 
Gene Names: Psmb4
EC: 3.4.25.1
UniProt
Find proteins for P34067 (Rattus norvegicus)
Explore P34067 
Go to UniProtKB:  P34067
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Israel636752
Israel Science FoundationIsrael300/17

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release