30SC | pdb_000030sc

Hairpin Inosine GCAA tetraloop

• PDB DOI: https://doi.org/10.2210/pdb30SC/pdb
• BMRB: 35053
• NAKB: 30SC

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2026-05-11 Released: 2026-07-22 
• Deposition Author(s): Mitteregger, C., Micura, R., Kreutz, C.
• Funding Organization(s): Austrian Science Fund, Austrian Research Promotion Agency

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

1-Deazainosine-impact on RNA structure and role in exploring ribozyme catalysis.

Mitteregger, C., Bereiter, R., Schramm, A., Ennifar, E., Kreutz, C., Micura, R.

(2026) Chem Sci 17: 13874-13883

• PubMed: 42266902 
• DOI: https://doi.org/10.1039/d6sc04009h
• Primary Citation Related Structures: 
  30SC


• PubMed Abstract: 
  

  Synthetic RNAs bearing deazapurine nucleobases are powerful probes for dissecting RNA-catalyzed reactions by atomic mutagenesis. Here we systematically characterize RNA containing 1-deazainosine (c ¹ I) and compare it with inosine (I). We first report the synthesis of a suitably protected c ¹ I phosphoramidite and its incorporation into RNA by solid-phase synthesis. We then provide a comprehensive thermodynamic analysis of base-pair stability from UV-melting experiments, showing that c ¹ I-C pairs are less stable than the corresponding I-C pairs. Although a two-hydrogen-bond Hoogsteen interaction between c ¹ I and protonated C is conceivable, NMR spectroscopy indicates that c ¹ I-C predominantly adopts a Watson-Crick-like geometry with a single hydrogen bond. These pairs are accommodated within RNA duplexes without disrupting neighboring base pairing. We also use c ¹ I to probe poly(I:C) motifs that mimic viral double-stranded RNA, assessing how strand length governs duplex versus hairpin formation. Finally, atomic mutagenesis of the twister ribozyme with c ¹ I supports the hypothesis that an active-site guanine participates directly in phosphodiester-bond cleavage. Together, these results clarify how deazapurines modulate nucleic-acid properties and provide guidance for their use in atomic mutagenesis to interrogate RNA catalysis.

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Organizational Affiliation: 
• Institute of Organic Chemistry, Center for Molecular Biosciences, Innsbruck (CMBI), University of Innsbruck Innrain 80-82 Innsbruck 6020 Austria ronald.micurauibk.ac.at.
Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de BiologieMoléculaire et Cellulaire, Université de Strasbourg Strasbourg 67000 France.

Biological Assembly 1  

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 4.82 kDa 
• Atom Count: 319 
• Modeled Residue Count: 15 
• Deposited Residue Count: 15 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*AP*AP*IP*GP*GP*CP*AP*AP*CP*CP*UP*UP*CP*G)-3')	A	15	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-22 
Deposition Author(s): Mitteregger, C., Micura, R., Kreutz, C.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	10.55776/P31691
Austrian Science Fund	Austria	10.55776/F80
Austrian Science Fund	Austria	10.55776/PAT4733025
Austrian Research Promotion Agency	Austria	858017

Revision History  

• Version 1.0: 2026-07-22
  Type: Initial release
  
• Version 1.1: 2026-08-05
  Changes: Database references