3HG6

Crystal Structure of the Recombinant Onconase from Rana pipiens

• PDB DOI: https://doi.org/10.2210/pdb3HG6/pdb

• Classification: HYDROLASE
• Organism(s): Lithobates pipiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-13 Released: 2010-05-19 
• Deposition Author(s): Camara-Artigas, A., Gavira, J.A., Casares-Atienza, S., Weininger, U., Balbach, J., Garcia-Mira, M.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.237 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Three-state thermal unfolding of onconase.

Casares-Atienza, S., Weininger, U., Camara-Artigas, A., Balbach, J., Garcia-Mira, M.M.

(2011) Biophys Chem 159: 267-274

• PubMed: 21840114 
• DOI: https://doi.org/10.1016/j.bpc.2011.07.005
• Primary Citation of Related Structures:  
  3HG6


• PubMed Abstract: 
  

  Onconase is a member of the ribonuclease A superfamily currently in phase IIIb clinical trials as a treatment for malign mesothelioma due to its cytotoxic activity selective against tumor-cells. In this work, we have studied the equilibrium thermal unfolding of onconase using a combination of several structural and biophysical techniques. Our results indicate that at least one significantly populated intermediate, which implies the exposure of hydrophobic surface and significant changes in the environment around Trp3, occurs during the equilibrium unfolding process of this protein. The intermediate begins to populate at about 30° below the global unfolding temperature, reaching a maximum population of nearly 60%, 10° below the global unfolding temperature.

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Organizational Affiliation: 

Departamento de Química Física, Facultad de Ciencias, Universidad de Granada. Avda. Fuentenueva s/n. 18071 Granada, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.32 kDa 
• Atom Count: 936 
• Modelled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Onconase	A	104	Lithobates pipiens	Mutation(s): 0  Gene Names: rpr EC: 3.1.27
UniProt
Find proteins for P22069 (Lithobates pipiens) Explore P22069  Go to UniProtKB:  P22069

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.237 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.516	α = 90
b = 39.799	β = 90
c = 68.536	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Camara-Artigas, A., Gavira, J.A., Casares-Atienza, S., Weininger, U., Balbach, J., Garcia-Mira, M.M.

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2023-11-08
  Changes: Database references
• Version 2.3: 2024-11-06
  Changes: Structure summary