9I8B | pdb_00009i8b

NMR-based model of an A-form 20mer dsRNA

• PDB DOI: https://doi.org/10.2210/pdb9I8B/pdb
• NAKB: 9I8B
• BMRB: 52888

• Classification: RNA
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2025-02-04 Released: 2025-03-12 
• Deposition Author(s): Mueller-Hermes, C., Sattler, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

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

Literature

Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA.

Muller-Hermes, C., Piomponi, V., Hilber, S., Asami, S., Kreutz, C., Bussi, G., Sattler, M.

(2025) Nucleic Acids Res 53

• PubMed: 40568935 
• DOI: https://doi.org/10.1093/nar/gkaf550
• Primary Citation Related Structures: 
  9I8B


• PubMed Abstract: 
  

  Adenosine-to-inosine (A-to-I) editing is a highly abundant modification of double-stranded RNA (dsRNA) and plays an important role in posttranscriptional gene regulation. Editing of multiple inosines by the ADAR1 enzyme leads to A-to-I hyper-editing of non-coding dsRNA, such as 3'UTRs, transposable elements, or foreign pathogenic RNAs, and is implicated in immune response and human diseases including cancer. The structural consequences of hyper-editing and its role in protein binding are poorly understood. Here, we combine solution nuclear magnetic resonance spectroscopy (NMR), biophysical methods such as small-angle X-ray scattering, and molecular dynamics simulations to study the sequence-dependent effects on conformation and dynamics of A-to-I hyper-editing for a 20-mer dsRNA and recognition of such RNAs by Endonuclease V. By comparing non-edited, single-edited, and hyper-edited dsRNA, we identify unique conformational features and extensive dynamics associated with hyper-editing, resulting in significantly increased base-pair opening. Hyper-edited dsRNA is more extended and adopts a highly dynamic ensemble of canonical and non-canonical conformations, which lead to preferential binding by Endonuclease V. Our integrated experimental and computational analysis identifies unique structural and dynamic features that are likely linked to specific protein recognition and the unique biological consequences of hyper-editing.

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Organizational Affiliation: 
• Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Garching, 85748, Germany.
Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany.
Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste, 34136, Italy.
Institute of Organic Chemistry and Center for Molecular Biosciences, Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020, Austria.
Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, 80802, Germany.

Biological Assembly 1  

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 12.77 kDa 
• Atom Count: 844 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*CP*UP*GP*GP*AP*CP*AP*AP*AP*UP*AP*CP*UP*CP*CP*GP*AP*GP*G)-3')	A	20	Rattus norvegicus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*CP*UP*CP*GP*GP*AP*GP*UP*AP*UP*UP*UP*GP*UP*CP*CP*AP*GP*U)-3')	B	20	Rattus norvegicus

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: 2025-03-12 
Deposition Author(s): Mueller-Hermes, C., Sattler, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Changes: Database references