5A5B

Structure of the 26S proteasome-Ubp6 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Characterization of the Interaction of Ubp6 with the 26S Proteasome.

Aufderheide, A.Beck, F.Stengel, F.Hartwig, M.Schweitzer, A.Pfeifer, G.Goldberg, A.L.Sakata, E.Baumeister, W.Forster, F.

(2015) Proc Natl Acad Sci U S A 112: 8626

  • DOI: 10.1073/pnas.1510449112
  • Primary Citation of Related Structures:  
    5A5B

  • PubMed Abstract: 
  • In eukaryotic cells, the 26S proteasome is responsible for the regulated degradation of intracellular proteins. Several cofactors interact transiently with this large macromolecular machine and modulate its function. The deubiquitylating enzyme ubiqu ...

    In eukaryotic cells, the 26S proteasome is responsible for the regulated degradation of intracellular proteins. Several cofactors interact transiently with this large macromolecular machine and modulate its function. The deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 [Ubp6; ubiquitin-specific protease (USP) 14 in mammals] is the most abundant proteasome-interacting protein and has multiple roles in regulating proteasome function. Here, we investigate the structural basis of the interaction between Ubp6 and the 26S proteasome in the presence and absence of the inhibitor ubiquitin aldehyde. To this end we have used single-particle electron cryomicroscopy in combination with cross-linking and mass spectrometry. Ubp6 binds to the regulatory particle non-ATPase (Rpn) 1 via its N-terminal ubiquitin-like domain, whereas its catalytic USP domain is positioned variably. Addition of ubiquitin aldehyde stabilizes the binding of the USP domain in a position where it bridges the proteasome subunits Rpn1 and the regulatory particle triple-A ATPase (Rpt) 1. The USP domain binds to Rpt1 in the immediate vicinity of the Ubp6 active site, which may effect its activation. The catalytic triad is positioned in proximity to the mouth of the ATPase module and to the deubiquitylating enzyme Rpn11, strongly implying their functional linkage. On the proteasome side, binding of Ubp6 favors conformational switching of the 26S proteasome into an intermediate-energy conformational state, in particular upon the addition of ubiquitin aldehyde. This modulation of the conformational space of the 26S proteasome by Ubp6 explains the effects of Ubp6 on the kinetics of proteasomal degradation.


    Organizational Affiliation

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de foerster@biochem.mpg.de.



Macromolecules
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PROTEASOME COMPONENT PRE31215Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PUP12261Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PUP33205Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT C114198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 5
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PROTEASOME COMPONENT PRE25287Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT C56241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PRE47266Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 8
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UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 68416Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
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UBIQUITIN ALDEHYDE976Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
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NIH Common Fund Data Resources
PHAROS  P62987
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PROTEASOME COMPONENT C7-ALPHAA252Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT Y7B250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT Y13C258Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PRE6D254Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PUP2E260Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PRE5F234Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT C1G288Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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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 
EC: 3.4.19.12
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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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Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
8L-PEPTIDE LINKINGC5 H11 N O2 SeMET
GLZ
Query on GLZ
9L-PEPTIDE LINKINGC2 H5 N OGLY
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2015-10-21
    Changes: Other
  • Version 1.3: 2017-08-30
    Changes: Data collection, Refinement description