9ZP2

E. coli RNA polymerase elongation complex containing the unnatural dP:Z*TP base pair in a trigger-loop-open conformation (b)

This is a non-PDB format compatible entry.

Summary for 9ZP2

• Entry DOI: 10.2210/pdb9zp2/pdb
• EMDB information: 74514
• Descriptor: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, DNA-directed RNA polymerase subunit beta, ... (11 entities in total)
• Functional Keywords: e. coli rna polymerase elongation complex containing the unnatural dp:z*tp base pair in a trigger-loop-open conformation (b), transcription, transcription-dna-rna complex, transcription/dna/rna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 382125.87

Authors

Li, Q.,Benner, S.A.,Wang, D. (deposition date: 2025-12-16, release date: 2026-07-29, Last modification date: 2026-09-16)

Primary citation

Li, Q.,Kim, H.J.,Liu, Y.,Oh, J.,Hou, P.,Hoshika, S.,Pintilie, G.,Aiyer, S.,Chong, J.,Lyumkis, D.,Benner, S.A.,Wang, D.
Structural basis of transcription of the hachimoji eight-letter alphabet by E. coli RNA polymerase.
Nat Commun, 17:-, 2026

PubMed Abstract: Expanded genetic alphabets with synthetic nucleotides can greatly increase the chemical diversity of nucleic acids, enabling new molecular functions. Because cellular transcription is executed by multi-subunit RNA polymerases, the compatibility of unnatural base pairs with this machinery is essential for engineering expanded genetic systems. Here we demonstrate that Escherichia coli RNA polymerase efficiently transcribes an eight-letter genetic alphabet with two orthogonal unnatural base pairs: P:Z and B:S pairs. To overcome G:Z misincorporation, we synthesize a higher-fidelity analogue, termed Z*, in which the C5 nitro group is replaced with a carboxamide. To elucidate substrate-recognition mechanisms, we determine four cryo-electron microscopy structures of RNA polymerase incorporating dZ:PTP or dP:Z*TP at 2.42-2.75 Å resolution. These structures, together with our early work on S:B pair, show that E. coli RNA polymerase is able to efficiently recognize these unnatural base pairs in the same manner as natural base pairs. Collectively, these results establish the feasibility of an eight-letter genetic alphabet for transcription.

PubMed: 42686745
DOI: 10.1038/s41467-026-76668-0

Experimental method

ELECTRON MICROSCOPY (2.64 Å)