4CR4

Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Deep Classification of a Large Cryo-Em Dataset Defines the Conformational Landscape of the 26S Proteasome.

Unverdorben, P., Beck, F., Sledz, P., Schweitzer, A., Pfeifer, G., Plitzko, J.M., Baumeister, W., Forster, F.

(2014) Proc Natl Acad Sci U S A 111: 5544

  • DOI: 10.1073/pnas.1403409111
  • Primary Citation of Related Structures:  
    4CR3, 4CR4, 4CR2

  • PubMed Abstract: 

    • The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently established by cryo-EM approaches. For a detailed underst ...

    The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently established by cryo-EM approaches. For a detailed understanding of the sequence of events from the initial binding of polyubiquitylated substrates to the translocation into the proteolytic core complex, it is necessary to move beyond static structures and characterize the conformational landscape of the 26S proteasome. To this end we have subjected a large cryo-EM dataset acquired in the presence of ATP and ATP-γS to a deep classification procedure, which deconvolutes coexisting conformational states. Highly variable regions, such as the density assigned to the largest subunit, Rpn1, are now well resolved and rendered interpretable. Our analysis reveals the existence of three major conformations: in addition to the previously described ATP-hydrolyzing (ATPh) and ATP-γS conformations, an intermediate state has been found. Its AAA-ATPase module adopts essentially the same topology that is observed in the ATPh conformation, whereas the lid is more similar to the ATP-γS bound state. Based on the conformational ensemble of the 26S proteasome in solution, we propose a mechanistic model for substrate recognition, commitment, deubiquitylation, and translocation into the core particle.

    Organizational Affiliation: 

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.



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PROTEASOME COMPONENT PRE31215Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PUP12261Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PUP33205Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT C114198Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PRE25287Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT C56241Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PRE47266Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT C7-ALPHAA252Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT Y7B250Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT Y13C258Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PUP2E260Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PRE5F234Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT C1G288Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOGH467Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 4 HOMOLOGI437Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 8 HOMOLOGJ405Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 6B HOMOLOGK428Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE SUBUNIT RPT4L437Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 6AM434Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN2N945Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN9O393Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN5P445Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN6Q434Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN7R429Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN3S523Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN12T274Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN8U338Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN11V306Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN10W268Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN13X156Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME COMPLEX SUBUNIT SEM1Y89Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN1Z993Saccharomyces cerevisiaeMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2014-04-30
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Data collection
  • Version 1.4: 2018-10-03
    Changes: Data collection