7QVE

Spinach 20S proteasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Cryo-EM structure of the plant 26S proteasome.

Kandolf, S.Grishkovskaya, I.Belacic, K.Bolhuis, D.L.Amann, S.Foster, B.Imre, R.Mechtler, K.Schleiffer, A.Tagare, H.D.Zhong, E.D.Meinhart, A.Brown, N.G.Haselbach, D.

(2022) Plant Commun 3: 100310-100310

  • DOI: https://doi.org/10.1016/j.xplc.2022.100310
  • Primary Citation of Related Structures:  
    7QVE

  • PubMed Abstract: 

    Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin-proteasome system. Thus, proteolysis by the 26S proteasome is vital to development, immunity, and cell division. Although the yeast and animal proteasomes are well characterized, there is only limited information on the plant proteasome. We determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy at an overall resolution of 3.3 Å. We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and yeast. Nevertheless, we noticed a structural difference in the proteolytic active β1 subunit. Furthermore, we uncovered an unseen compression state by characterizing the proteasome's conformational landscape. We suspect that this new conformation of the 20S core protease, in correlation with a partial opening of the unoccupied gate, may contribute to peptide release after proteolysis. Our data provide a structural basis for the plant proteasome, which is crucial for further studies.


  • Organizational Affiliation

    Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeA [auth i],
H [auth C]
235Spinacia oleraceaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeB [auth j],
I [auth D]
250Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P52427 (Spinacia oleracea)
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UniProt GroupP52427
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeC [auth k],
J [auth E]
247Spinacia oleraceaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeD [auth l],
K [auth F]
237Spinacia oleraceaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeE [auth m],
L [auth G]
274Spinacia oleraceaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3F [auth n],
M [auth X]
249Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for O24362 (Spinacia oleracea)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeBA [auth h],
G [auth B]
246Spinacia oleraceaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaN [auth o],
U [auth a]
236Spinacia oleraceaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaO [auth p],
V [auth b]
274Spinacia oleraceaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaP [auth q],
W [auth c]
204Spinacia oleraceaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaQ [auth r],
X [auth d]
209Spinacia oleraceaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5R [auth s],
Y [auth e]
272Spinacia oleraceaMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for O24361 (Spinacia oleracea)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaS [auth t],
Z [auth f]
223Spinacia oleraceaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth g],
T [auth u]
240Spinacia oleraceaMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
RECONSTRUCTIONcryoSPARC3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references