7YPK

Close-ring hexamer of the substrate-bound Lon protease with an S678A mutation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A 5+1 assemble-to-activate mechanism of the Lon proteolytic machine.

Li, S.Hsieh, K.Y.Kuo, C.I.Lin, T.C.Lee, S.H.Chen, Y.R.Wang, C.H.Ho, M.R.Ting, S.Y.Zhang, K.Chang, C.I.

(2023) Nat Commun 14: 7340-7340

  • DOI: https://doi.org/10.1038/s41467-023-43035-2
  • Primary Citation of Related Structures:  
    7YPH, 7YPI, 7YPJ, 7YPK, 7YUH, 7YUM, 7YUP, 7YUT, 7YUU, 7YUV, 7YUW, 7YUX, 8K3Y

  • PubMed Abstract: 

    Many AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In this ATP-dependent translocating state, the substrate is gripped by the pore loops of the ATPase domains arranged in a universal right-handed spiral staircase organization. However, the process by which a AAA+ protein is activated to adopt this substrate-pore-loop arrangement remains unknown. We show here, using cryo-electron microscopy (cryo-EM), that the activation process of the Lon AAA+ protease may involve a pentameric assembly and a substrate-dependent incorporation of the sixth protomer to form the substrate-pore-loop contacts seen in the translocating state. Based on the structural results, we design truncated monomeric mutants that inhibit Lon activity by binding to the native pentamer and demonstrated that expressing these monomeric mutants in Escherichia coli cells containing functional Lon elicits specific phenotypes associated with lon deficiency, including the inhibition of persister cell formation. These findings uncover a substrate-dependent assembly process for the activation of a AAA+ protein and demonstrate a targeted approach to selectively inhibit its function within cells.


  • Organizational Affiliation

    Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China. lishanshan@ustc.edu.cn.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alpha-S1-caseinA [auth S]19Bos taurusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lon protease793Meiothermus taiwanensisMutation(s): 1 
Gene Names: lonA1lonlon1_1
EC: 3.4.21.53
UniProt
Find proteins for A0A059VAZ3 (Meiothermus taiwanensis)
Explore A0A059VAZ3 
Go to UniProtKB:  A0A059VAZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059VAZ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2
MODEL REFINEMENTPHENIX1.18.2_3874
MODEL REFINEMENTCoot0.9.6

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan108-2320-B-001-011-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Database references