7OR6 | pdb_00007or6

The crystal structure of the domain-swapped dimer of onconase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.243 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The crystal structure of the domain-swapped dimer of onconase highlights some catalytic and antitumor activity features of the enzyme.

Gotte, G.Campagnari, R.Loreto, D.Bettin, I.Calzetti, F.Menegazzi, M.Merlino, A.

(2021) Int J Biol Macromol 191: 560-571

  • DOI: https://doi.org/10.1016/j.ijbiomac.2021.09.095
  • Primary Citation Related Structures: 
    7OR6, 7ORD

  • PubMed Abstract: 

    Onconase (ONC) is a monomeric amphibian "pancreatic-type" RNase endowed with remarkable anticancer activity. ONC spontaneously forms traces of a dimer (ONC-D) in solution, while larger amounts can be formed when ONC is lyophilized from mildly acidic solutions. Here, we report the crystal structure of ONC-D and analyze its catalytic and antitumor activities in comparison to ONC. ONC-D forms via the three-dimensional swapping of the N-terminal α-helix between two monomers, but it displays a significantly different quaternary structure from that previously modeled [Fagagnini A et al., 2017, Biochem J 474, 3767-81], and based on the crystal structure of the RNase A N-terminal swapped dimer. ONC-D presents a variable quaternary assembly deriving from a variable open interface, while it retains a catalytic activity that is similar to that of ONC. Notably, ONC-D displays antitumor activity against two human melanoma cell lines, although it exerts a slightly lower cytostatic effect than the monomer. The inhibition of melanoma cell proliferation by ONC or ONC-D is associated with the reduction of the expression of the anti-apoptotic B cell lymphoma 2 (Bcl2), as well as of the total expression and phosphorylation of the Signal Transducer and Activator of Transcription (STAT)-3. Phosphorylation is inhibited in both STAT3 Tyr705 and Ser727 key-residues, as well as in its upstream tyrosine-kinase Src. Consequently, both ONC species should exert their anti-cancer action by inhibiting the pro-tumor pleiotropic STAT3 effects deriving either by its phospho-tyrosine activation or by its non-canonical signaling pathways. Both ONC species, indeed, increase the portion of A375 cells undergoing apoptotic cell death. This study expands the variety of RNase domain-swapped dimeric structures, underlining the unpredictability of the open interface arrangement upon domain swapping. Structural data also offer valuable insights to analyze the differences in the measured ONC or ONC-D biological activities.


  • Organizational Affiliation
    • Department of Neuroscience, Biomedicine and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy. Electronic address: giovanni.gotte@univr.it.

Macromolecule Content 

  • Total Structure Weight: 23.95 kDa 
  • Atom Count: 1,785 
  • Modeled Residue Count: 208 
  • Deposited Residue Count: 210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein P-30A [auth AAA],
B [auth BBB]
105Lithobates pipiensMutation(s): 0 
EC: 3.1.27
UniProt
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
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth AAA],
B [auth BBB]
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.243 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.29α = 90
b = 60.05β = 90
c = 101.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary