Crystal structure of Lon protease from Thermococcus onnurineus NA1

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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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:  

  • 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

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 
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
C10 H15 N5 O10 P2
Query on PE8

Download Ideal Coordinates CCD File 
D [auth A]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
Query on PE4

Download Ideal Coordinates CCD File 
C16 H34 O8
Binding Affinity Annotations 
IDSourceBinding Affinity
ADP PDBBind:  3K1J Kd: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • 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
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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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