PDBsum entry 2dzn

Go to PDB code: 
protein Protein-protein interface(s) links
Protein binding PDB id
Protein chains
226 a.a. *
57 a.a. *
67 a.a. *
Waters ×472
* Residue conservation analysis
PDB id:
Name: Protein binding
Title: Crystal structure analysis of yeast nas6p complexed with the proteasome subunit, rpt3
Structure: Probable 26s proteasome regulatory subunit p28. Chain: a, c, e. Synonym: nas6p, proteasome non-atpase subunit 6. Engineered: yes. 26s protease regulatory subunit 6b homolog. Chain: b, d, f. Fragment: c-terminal domain. Synonym: rpt3, protein ynt1, tat-binding homolog 2. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.20Å     R-factor:   0.197     R-free:   0.265
Authors: S.Yokoyama,B.Padmanabhan,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref: Y.Nakamura et al. (2007). Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome. Biochem Biophys Res Commun, 359, 503-509. PubMed id: 17555716 DOI: 10.1016/j.bbrc.2007.05.138
29-Sep-06     Release date:   17-Jul-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P50086  (PSD10_YEAST) -  Probable 26S proteasome regulatory subunit p28
228 a.a.
226 a.a.
Protein chain
Pfam   ArchSchema ?
P33298  (PRS6B_YEAST) -  26S protease regulatory subunit 6B homolog
428 a.a.
57 a.a.
Protein chains
Pfam   ArchSchema ?
P33298  (PRS6B_YEAST) -  26S protease regulatory subunit 6B homolog
428 a.a.
67 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     proteasome regulatory particle   3 terms 
  Biological process     proteolysis   2 terms 
  Biochemical function     molecular_function     2 terms  


DOI no: 10.1016/j.bbrc.2007.05.138 Biochem Biophys Res Commun 359:503-509 (2007)
PubMed id: 17555716  
Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome.
Y.Nakamura, T.Umehara, A.Tanaka, M.Horikoshi, B.Padmanabhan, S.Yokoyama.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20541423 N.Gallastegui, and M.Groll (2010).
The 26S proteasome: assembly and function of a destructive machine.
  Trends Biochem Sci, 35, 634-642.  
19489727 D.Finley (2009).
Recognition and processing of ubiquitin-protein conjugates by the proteasome.
  Annu Rev Biochem, 78, 477-513.  
19653995 F.Förster, K.Lasker, F.Beck, S.Nickell, A.Sali, and W.Baumeister (2009).
An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.
  Biochem Biophys Res Commun, 388, 228-233.  
19412159 J.Roelofs, S.Park, W.Haas, G.Tian, F.E.McAllister, Y.Huo, B.H.Lee, F.Zhang, Y.Shi, S.P.Gygi, and D.Finley (2009).
Chaperone-mediated pathway of proteasome regulatory particle assembly.
  Nature, 459, 861-865.  
19516331 K.Madura (2009).
Cell biology: The proteasome assembly line.
  Nature, 459, 787-788.  
19446322 M.Funakoshi, R.J.Tomko, H.Kobayashi, and M.Hochstrasser (2009).
Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base.
  Cell, 137, 887-899.  
19412160 S.Park, J.Roelofs, W.Kim, J.Robert, M.Schmidt, S.P.Gygi, and D.Finley (2009).
Hexameric assembly of the proteasomal ATPases is templated through their C termini.
  Nature, 459, 866-870.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.