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 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 ...

    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.



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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME COMPONENT PRE3A [auth 1]215Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 2
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PROTEASOME COMPONENT PUP1B [auth 2]261Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PUP3C [auth 3]205Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 4
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PROTEASOME COMPONENT C11D [auth 4]198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PRE2E [auth 5]287Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 6
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PROTEASOME COMPONENT C5F [auth 6]241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PRE4G [auth 7]266Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 8
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UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6H [auth 8]416Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
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Entity ID: 9
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UBIQUITIN ALDEHYDEI [auth 9]76Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
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PROTEASOME COMPONENT C7-ALPHAJ [auth A]252Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT Y7K [auth B]250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT Y13L [auth C]258Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PRE6M [auth D]254Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PUP2N [auth E]260Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT PRE5O [auth F]234Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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PROTEASOME COMPONENT C1P [auth G]288Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOGQ [auth H]467Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 4 HOMOLOGR [auth I]437Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 8 HOMOLOGS [auth J]405Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 6B HOMOLOGT [auth K]428Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE SUBUNIT RPT4U [auth L]437Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASE REGULATORY SUBUNIT 6AV [auth M]434Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN2W [auth N]945Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN9X [auth O]393Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN5Y [auth P]445Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN6Z [auth Q]434Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN7AA [auth R]429Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN3BA [auth S]523Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN12CA [auth T]274Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN8DA [auth U]338Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN11EA [auth V]306Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.19.12
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26S PROTEASOME REGULATORY SUBUNIT RPN10FA [auth W]268Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN13GA [auth X]156Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME COMPLEX SUBUNIT SEM1HA [auth Y]89Saccharomyces cerevisiaeMutation(s): 0 
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26S PROTEASOME REGULATORY SUBUNIT RPN1IA [auth Z]993Saccharomyces cerevisiaeMutation(s): 0 
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Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
H [auth 8]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
GLZ
Query on GLZ
I [auth 9]L-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  (Full details and data files)

  • 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