4JPO

5A resolution structure of Proteasome Assembly Chaperone Hsm3 in complex with a C-terminal fragment of Rpt1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Reconfiguration of the proteasome during chaperone-mediated assembly.

Park, S.Li, X.Kim, H.M.Singh, C.R.Tian, G.Hoyt, M.A.Lovell, S.Battaile, K.P.Zolkiewski, M.Coffino, P.Roelofs, J.Cheng, Y.Finley, D.

(2013) Nature 497: 512-516

  • DOI: https://doi.org/10.1038/nature12123
  • Primary Citation of Related Structures:  
    4JPO

  • PubMed Abstract: 

    The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting into pockets of the α-ring. Rpt ring assembly is mediated by four chaperones, each binding a distinct Rpt subunit. Here we report that the base subassembly of the Saccharomyces cerevisiae proteasome, which includes the Rpt ring, forms a high-affinity complex with the CP. This complex is subject to active dissociation by the chaperones Hsm3, Nas6 and Rpn14. Chaperone-mediated dissociation was abrogated by a non-hydrolysable ATP analogue, indicating that chaperone action is coupled to nucleotide hydrolysis by the Rpt ring. Unexpectedly, synthetic Rpt tail peptides bound α-pockets with poor specificity, except for Rpt6, which uniquely bound the α2/α3-pocket. Although the Rpt6 tail is not visualized within an α-pocket in mature proteasomes, it inserts into the α2/α3-pocket in the base-CP complex and is important for complex formation. Thus, the Rpt-CP interface is reconfigured when the lid complex joins the nascent proteasome to form the mature holoenzyme.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA mismatch repair protein HSM3
A, B
491Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HSM3YBR272CYBR1740
UniProt
Find proteins for P38348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38348 
Go to UniProtKB:  P38348
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38348
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 7 homolog
C, D
100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1CIM5YTA3YKL145W
UniProt
Find proteins for P33299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33299 
Go to UniProtKB:  P33299
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33299
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.299α = 90
b = 185.299β = 90
c = 357.382γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Database references
  • Version 1.2: 2013-07-10
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2020-02-26
    Changes: Data collection, Database references
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Refinement description