RNASE 3/1 version3

Experimental Data Snapshot

  • Resolution: 1.51 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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Exploring the RNase A scaffold to combine catalytic and antimicrobial activities. Structural characterization of RNase 3/1 chimeras.

Fernandez-Millan, P.Vazquez-Monteagudo, S.Boix, E.Prats-Ejarque, G.

(2022) Front Mol Biosci 9: 964717-964717

  • DOI: https://doi.org/10.3389/fmolb.2022.964717
  • Primary Citation of Related Structures:  
    6SSN, 6YBC, 6YBE, 6YMT

  • PubMed Abstract: 

    Design of novel antibiotics to fight antimicrobial resistance is one of the first global health priorities. Novel protein-based strategies come out as alternative therapies. Based on the structure-function knowledge of the RNase A superfamily we have engineered a chimera that combines RNase 1 highest catalytic activity with RNase 3 unique antipathogen properties. A first construct (RNase 3/1-v1) was successfully designed with a catalytic activity 40-fold higher than RNase 3, but alas in detriment of its anti-pathogenic activity. Next, two new versions of the original chimeric protein were created showing improvement in the antimicrobial activity. Both second generation versions (RNases 3/1-v2 and -v3) incorporated a loop characteristic of RNase 3 (L7), associated to antimicrobial activity. Last, removal of an RNase 1 flexible loop (L1) in the third version enhanced its antimicrobial properties and catalytic efficiency. Here we solved the 3D structures of the three chimeras at atomic resolution by X-ray crystallography. Structural analysis outlined the key functional regions. Prediction by molecular docking of the protein chimera in complex with dinucleotides highlighted the contribution of the C-terminal region to shape the substrate binding cavity and determine the base selectivity and catalytic efficiency. Nonetheless, the structures that incorporated the key features related to RNase 3 antimicrobial activity retained the overall RNase 1 active site conformation together with the essential structural elements for binding to the human ribonuclease inhibitor (RNHI), ensuring non-cytotoxicity. Results will guide us in the design of the best RNase pharmacophore for anti-infective therapies.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNase 3/1 version3
A, B
130synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
O4 P
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.51 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.381α = 73.61
b = 39.548β = 83.11
c = 46.331γ = 66.64
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainSAF2015-66007-P

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references