3K1J

Crystal structure of Lon protease from Thermococcus onnurineus NA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.235 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber

Cha, S.S.An, Y.J.Lee, C.R.Lee, H.S.Kim, Y.G.Kim, S.J.Kwon, K.K.De Donatis, G.M.Lee, J.H.Maurizi, M.R.Kang, S.G.

(2010) EMBO J 29: 3520-3530

  • DOI: https://doi.org/10.1038/emboj.2010.226
  • Primary Citation of Related Structures:  
    3K1J

  • PubMed Abstract: 

    Lon proteases are distributed in all kingdoms of life and are required for survival of cells under stress. Lon is a tandem fusion of an AAA+ molecular chaperone and a protease with a serine-lysine catalytic dyad. We report the 2.0-Å resolution crystal structure of Thermococcus onnurineus NA1 Lon (TonLon). The structure is a three-tiered hexagonal cylinder with a large sequestered chamber accessible through an axial channel. Conserved loops extending from the AAA+ domain combine with an insertion domain containing the membrane anchor to form an apical domain that serves as a gate governing substrate access to an internal unfolding and degradation chamber. Alternating AAA+ domains are in tight- and weak-binding nucleotide states with different domain orientations and intersubunit contacts, reflecting intramolecular dynamics during ATP-driven protein unfolding and translocation. The bowl-shaped proteolytic chamber is contiguous with the chaperone chamber allowing internalized proteins direct access to the proteolytic sites without further gating restrictions.


  • Organizational Affiliation

    Marine Biotechnology Research Center, Korea Ocean Research and Development Institute, Ansan, Republic of Korea. chajung@kordi.re.kr


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent protease Lon
A, B
604Thermococcus onnurineus NA1Mutation(s): 2 
UniProt
Find proteins for B6YU74 (Thermococcus onnurineus (strain NA1))
Explore B6YU74 
Go to UniProtKB:  B6YU74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YU74
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.235 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.454α = 90
b = 121.454β = 90
c = 195.24γ = 120
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary