2Z5C

Crystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes

Yashiroda, H.Mizushima, T.Okamoto, K.Kameyama, T.Hayashi, H.Kishimoto, T.Niwa, S.Kasahara, M.Kurimoto, E.Sakata, E.Takagi, K.Suzuki, A.Hirano, Y.Murata, S.Kato, K.Yamane, T.Tanaka, K.

(2008) Nat.Struct.Mol.Biol. 15: 228-236

  • DOI: 10.1038/nsmb.1386
  • Primary Citation of Related Structures:  2Z5B, 2Z5E

  • PubMed Abstract: 
  • Eukaryotic 20S proteasomes are composed of two alpha-rings and two beta-rings, which form an alphabetabetaalpha stacked structure. Here we describe a proteasome-specific chaperone complex, designated Dmp1-Dmp2, in budding yeast. Dmp1-Dmp2 directly bo ...

    Eukaryotic 20S proteasomes are composed of two alpha-rings and two beta-rings, which form an alphabetabetaalpha stacked structure. Here we describe a proteasome-specific chaperone complex, designated Dmp1-Dmp2, in budding yeast. Dmp1-Dmp2 directly bound to the alpha5 subunit to facilitate alpha-ring formation. In Deltadmp1 cells, alpha-rings lacking alpha4 and decreased formation of 20S proteasomes were observed. Dmp1-Dmp2 interacted with proteasome precursors early during proteasome assembly and dissociated from the precursors before the formation of half-proteasomes. Notably, the crystallographic structures of Dmp1 and Dmp2 closely resemble that of PAC3-a mammalian proteasome-assembling chaperone; nonetheless, neither Dmp1 nor Dmp2 showed obvious sequence similarity to PAC3. The structure of the Dmp1-Dmp2-alpha5 complex reveals how this chaperone functions in proteasome assembly and why it dissociates from proteasome precursors before the beta-rings are assembled.


    Organizational Affiliation

    Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, Bunkyo-ku, Tokyo 113-8613, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein YPL144W
A, D
151Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: POC4 (DMP1)
Find proteins for Q12245 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12245
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein YLR021W
B, E
149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: IRC25 (DMP2, POC3)
Find proteins for Q07951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07951
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP2
C, F
262Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 158.687α = 90.00
b = 159.181β = 90.00
c = 65.035γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-09
    Type: Data collection, Source and taxonomy