Crystal structure of Onconase C87A/C104A-ONC

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report

This is version 2.2 of the entry. See complete history


Impact of the C-terminal disulfide bond on the folding and stability of onconase.

Schulenburg, C.Weininger, U.Neumann, P.Meiselbach, H.Stubbs, M.T.Sticht, H.Balbach, J.Ulbrich-Hofmann, R.Arnold, U.

(2010) Chembiochem 11: 978-986

  • DOI: https://doi.org/10.1002/cbic.200900773
  • Primary Citation of Related Structures:  
    2KB6, 3FD7

  • PubMed Abstract: 

    The two homologous proteins ribonuclease A and onconase fold through conserved initial contacts but differ significantly in their thermodynamic stability. A disulfide bond is located in the folding initiation site of onconase (the C-terminal part of the protein molecule) that is missing in ribonuclease A, whereas the other three disulfide bonds of onconase are conserved in ribonuclease A. Consequently, the deletion of this C-terminal disulfide bond (C87-C104) allows the impact of the contacts in this region on the folding of onconase to be studied. We found the C87A/C104A-onconase variant to be less active and less stable than the wild-type protein, whereas the tertiary structure, which was determined by both X-ray crystallography and NMR spectroscopy, was only marginally affected. The folding kinetics of the variant, however, were found to be changed considerably in comparison to wild-type onconase. Proton exchange experiments in combination with two-dimensional NMR spectroscopy revealed differences in the native-state dynamics of the two proteins in the folding initiation site, which are held responsible for the changed folding mechanism. Likewise, the molecular dynamics simulation of the unfolding reaction indicated disparities for both proteins. Our results show that the high stability of onconase is based on the efficient stabilization of the folding initiation site by the C-terminal disulfide bond. The formation of the on-pathway intermediate, which is detectable during the folding of the wild-type protein and promotes the fast and efficient refolding reaction, requires the presence of this covalent bond.

  • Organizational Affiliation

    Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein P-30
A, B
104Lithobates pipiensMutation(s): 2 
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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
I [auth A]
J [auth A]
C [auth A],
D [auth A],
E [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth B]
C3 H8 O3
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]1,2-ETHANEDIOL
C2 H6 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PCA
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.46α = 90
b = 51.19β = 90
c = 87.69γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence
  • Version 2.1: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 2.2: 2023-11-01
    Changes: Data collection, Refinement description