2DZN

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome

Nakamura, Y.Umehara, T.Tanaka, A.Horikoshi, M.Padmanabhan, B.Yokoyama, S.

(2007) Biochem Biophys Res Commun 359: 503-509

  • DOI: 10.1016/j.bbrc.2007.05.138
  • Primary Citation of Related Structures:  
    2DZN

  • PubMed Abstract: 
  • The 26S proteasome-dependent protein degradation is an evolutionarily conserved process. The mammalian oncoprotein gankyrin, which associates with S6 of the proteasome, facilitates the degradation of pRb, and thus possibly acts as a bridging factor betwe ...

    The 26S proteasome-dependent protein degradation is an evolutionarily conserved process. The mammalian oncoprotein gankyrin, which associates with S6 of the proteasome, facilitates the degradation of pRb, and thus possibly acts as a bridging factor between the proteasome and its substrates. However, the mechanism of the proteasome-dependent protein degradation in yeast is poorly understood. Here, we report the tertiary structure of the complex between Nas6 and a C-terminal domain of Rpt3, which are the yeast orthologues of gankyrin and S6, respectively. The concave region of Nas6 bound to the alpha-helical domain of Rpt3. The stable interaction between Nas6 and Rpt3 was mediated by intermolecular interactions composed of complementary charged patches. The recognition of Rpt3 by Nas6 in the crystal suggests that Nas6 is indeed a subunit of the 26S proteasome. These results provide a structural basis for the association between Nas6 and the heterohexameric ATPase ring of the proteasome through Rpt3.


    Organizational Affiliation

    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable 26S proteasome regulatory subunit p28 ACE228Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P50086 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50086 
Go to UniProtKB:  P50086
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 6B homolog BDF82Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33298 
Go to UniProtKB:  P33298
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.376α = 90
b = 100.22β = 94.7
c = 72.203γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance