4CR3

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.30 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:  
    4CR2, 4CR3, 4CR4

  • 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 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 ...

    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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EC: 3.4.25.1
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PROTEASOME COMPONENT PUP1B [auth 2]261Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PUP3C [auth 3]205Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PRE2E [auth 5]287Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT C5F [auth 6]241Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT PRE4G [auth 7]266Saccharomyces cerevisiaeMutation(s): 0 
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PROTEASOME COMPONENT C7-ALPHAH [auth A]252Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOGO [auth H]467Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 4 HOMOLOGP [auth I]437Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 6B HOMOLOGR [auth K]428Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE SUBUNIT RPT4S [auth L]437Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN2U [auth N]945Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN9V [auth O]393Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN5W [auth P]445Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN6X [auth Q]434Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN7Y [auth R]429Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN11CA [auth V]306Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN10DA [auth W]268Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN13EA [auth X]156Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME COMPLEX SUBUNIT SEM1FA [auth Y]89Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN1GA [auth Z]993Saccharomyces cerevisiaeMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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