3K1J | pdb_00003k1j

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), 0.234 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

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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 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

Macromolecule Content 

  • Total Structure Weight: 135.14 kDa 
  • Atom Count: 9,587 
  • Modeled Residue Count: 1,127 
  • Deposited Residue Count: 1,208 
  • Unique protein chains: 1

Macromolecules

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|  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), 0.234 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.205 (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

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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
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary