3WHL

Crystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Proteasome Formation Controlled by an Assembly Chaperone Nas2

Satoh, T.Saeki, Y.Hiromoto, T.Wang, Y.H.Uekusa, Y.Yagi, H.Yoshihara, H.Yagi-Utsumi, M.Mizushima, T.Tanaka, K.Kato, K.

(2014) Structure --: --

  • DOI: 10.1016/j.str.2014.02.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteasome formation does not occur due to spontaneous self-organization but results from a highly ordered process assisted by several assembly chaperones. The assembly of the proteasome ATPase subunits is assisted by four client-specific chaperones, ...

    Proteasome formation does not occur due to spontaneous self-organization but results from a highly ordered process assisted by several assembly chaperones. The assembly of the proteasome ATPase subunits is assisted by four client-specific chaperones, of which three have been structurally resolved. Here, we provide the structural basis for the working mechanisms of the last, hereto structurally uncharacterized assembly chaperone, Nas2. We revealed that Nas2 binds to the Rpt5 subunit in a bivalent mode: the N-terminal helical domain of Nas2 masks the Rpt1-interacting surface of Rpt5, whereas its C-terminal PDZ domain caps the C-terminal proteasome-activating motif. Thus, Nas2 operates as a proteasome activation blocker, offering a checkpoint during the formation of the 19S ATPase prior to its docking onto the proteolytic 20S core particle.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
A, C, E, G
270Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
This entity is chimeric
Mutation(s): 0 
Gene Names: RPT5 (YTA1), pan
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33297
Find proteins for Q8U4H3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U4H3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable 26S proteasome regulatory subunit p27
B, D, F, H
122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NAS2
Find proteins for P40555 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40555
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, C, E, G
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.630α = 90.00
b = 110.630β = 90.00
c = 251.940γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy