Onconase, atomic resolution crystal structure

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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Crystal structure of Onconase at 1.1 angstrom resolution--insights into substrate binding and collective motion.

Holloway, D.E.Singh, U.P.Shogen, K.Acharya, K.R.

(2011) FEBS J 278: 4136-4149

  • DOI: https://doi.org/10.1111/j.1742-4658.2011.08320.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Onconase(®) (ONC) is an amphibian member of the pancreatic ribonuclease superfamily that is selectively toxic to tumor cells. It is a much less efficient enzyme than the archetypal ribonuclease A and, in an attempt to gain further insight, we report the first atomic resolution crystal structure of ONC, determined in complex with sulfate ions at 100 K. The electron density map is of a quality sufficient to reveal significant nonplanarity in several peptide bonds. The majority of active site residues are very well defined, with the exceptions being Lys31 from the catalytic triad and Lys33 from the B(1) subsite, which are relatively mobile but rigidify upon nucleotide binding. Cryocooling causes a compaction of the unit cell and the protein contained within. This is principally the result of an inward movement of one of the lobes of the enzyme (lobe 2), which also narrows the active site cleft. Binding a nucleotide in place of sulfate is associated with an approximately perpendicular movement of lobe 2 and has little further effect on the cleft width. Aspects of this deformation are present in the principal axes of anisotropy extracted from C(α) atomic displacement parameters, indicating its intrinsic nature. The three lowest-frequency modes of ONC motion predicted by an anisotropic network model are compaction/expansion variations in which lobe 2 is the prime mover. Two of these have high similarity to the cryocooling response and imply that the essential 'breathing' motion of ribonuclease A is conserved in ONC. Instead, shifts in conformational equilibria may contribute to the reduced ribonucleolytic activity of ONC.

  • Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, Bath, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein P-30104Lithobates pipiensMutation(s): 0 
EC: 3.1.27
Find proteins for P22069 (Lithobates pipiens)
Explore P22069 
Go to UniProtKB:  P22069
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22069
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.234α = 90
b = 38.157β = 90
c = 68.917γ = 90
Software Package:
Software NamePurpose
HKL-2000data 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: 2011-10-05
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description