9JWA | pdb_00009jwa

Crystal Structure of Lon Bound to a Substrate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.249 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the allosteric activation of Lon by the heat shock protein LarA.

Wang, H.J.Kuan, Y.E.Ho, M.R.Chang, C.I.

(2025) Nat Commun 16: 2212-2212

  • DOI: https://doi.org/10.1038/s41467-025-57482-6
  • Primary Citation of Related Structures:  
    9JWA

  • PubMed Abstract: 

    Lon is a conserved AAA+ (ATPases associated with diverse cellular activities) proteolytic machine that plays a key regulatory role in cells under proteotoxic stress. Lon-mediated proteolysis can be stimulated by either the unfolded or specific protein substrates accumulated under stress conditions. However, the molecular basis for this substrate-controlled proteolysis remains unclear. Here, we have found that the heat shock protein LarA, a recently discovered Lon substrate and allosteric activator, binds to the N-terminal domain (NTD) of Lon. The crystal structure of the LarA-NTD complex shows that LarA binds to a highly conserved groove in the NTD through the terminal aromatic residue of its C-terminal degron. Crystallographic and biochemical evidence further reveals that this binding exposes the hydrophobic core of LarA, which can bind a leucine residue and promote local protein unfolding. These results define the mechanistic role of the NTD in regulating Lon-mediated proteolysis in response to varying cellular conditions.


  • Organizational Affiliation
    • Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF1150 domain-containing protein
A, C
95Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: CC_3593
UniProt
Find proteins for Q9A2G8 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15))
Explore Q9A2G8 
Go to UniProtKB:  Q9A2G8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A2G8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lon protease
B, D
206Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: lonCC_1960
EC: 3.4.21.53
UniProt
Find proteins for P0CAW0 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15))
Explore P0CAW0 
Go to UniProtKB:  P0CAW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CAW0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.249 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.05α = 90
b = 81.05β = 90
c = 104.569γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Council (NSC, Taiwan)TaiwanNSTC- 110- 2811 -B-001-071

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references