9TCG

Crystal Structure of a prebiotic tRNA acceptor stem mimic

Summary for 9TCG

• Entry DOI: 10.2210/pdb9tcg/pdb
• Descriptor: RNA (5'-R(P*AP*GP*CP*GP*A)-3'), RNA (5'-R(*UP*CP*GP*CP*UP*UP*(5BU)P*CP*C)-3') (2 entities in total)
• Functional Keywords: anomalous scattering; nucleic acids, prebiotic trna acceptor stem, rna triplex, rna
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 9525.58

Authors

Bellini, D.,Liu, Z.W.,El Omari, K. (deposition date: 2025-11-21, release date: 2026-02-11)

Primary citation

Liu, Z.,Bellini, D.,Gorrec, F.,Wagner, A.,El Omari, K.,Sutherland, J.D.
Crystal structure of a tRNA acceptor-stem mimic at 1.94 angstrom resolution.
Acta Crystallogr.,Sect.F, 82:57-65, 2026

PubMed Abstract: Despite the theoretical advantages of phosphorus single-wavelength anomalous diffraction (P-SAD) for nucleic acid phasing, its application remains limited due to high atomic displacement parameters and an unfavourable ratio of unique reflections to anomalous scatterers. In this study, we report the crystal structure of an RNA complex composed of four strands, which was solved by experimental phasing after AlphaFold3 failed to produce reliable models. Bromine single-wavelength anomalous diffraction (Br-SAD) data were collected at 0.916 Å on beamline I04 at Diamond Light Source, while phosphorus anomalous data were obtained at 3.024 Å on beamline I23. The structure was successfully phased using bromine anomalous scattering, and phosphorus anomalous peaks corroborated the backbone positions and validated the model. Attempts to phase the structure directly from phosphorus data failed, consistent with theoretical predictions that successful SAD phasing requires a significantly higher reflection-to-scatterer ratio. The final models reveal an RNA complex stabilized by Watson-Crick and Hoogsteen base pairing, forming a pseudo-helical complex instead of the anticipated hairpin stem-loop, likely reflecting crystallization artefacts. This work demonstrates the complementary use of bromine and phosphorus anomalous signals in RNA crystallography.

PubMed: 41608807
DOI: 10.1107/S2053230X26000658

Experimental method

X-RAY DIFFRACTION (2.52 Å)