12EI
Pre-translocated RNA polymerase elemental paused elongation complex, TL closed (ePEC closed)
Summary for 12EI
| Entry DOI | 10.2210/pdb12ei/pdb |
| EMDB information | 76378 |
| Descriptor | DNA non-template strand, ZINC ION, DNA template strand, ... (11 entities in total) |
| Functional Keywords | elongation, pausing, pause escape, ppgpp, stringent response, transcription, transcription-dna-rna complex, transcription/dna/rna |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 8 |
| Total formula weight | 441846.70 |
| Authors | |
| Primary citation | Mueller, A.U.,Mooney, R.A.,Engstrom, M.D.,Bao, Y.,Wolfe, M.B.,Sah, B.,Buscher, J.,Saba, J.,Liu, J.,Darst, S.A.,Landick, R. ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition. Biorxiv, 2026 Cited by PubMed Abstract: The signaling molecules guanosine 5'-tri/diphosphate 3'-diphosphate, (p)ppGpp, control bacterial protein synthesis rates and cell growth by targeting transcription, translation, NTP synthesis, and other functions. In lineages like , (p)ppGpp produced in response to charged-tRNA deficiency directly targets transcribing RNAP polymerase (RNAP) to match its pace to the pioneering ribosome on the nascent RNA (transcription-translation coupling). However, the mechanism by which (p)ppGpp slows RNAP is poorly defined. (p)ppGpp may allosterically stimulate RNAP pausing, inhibit catalysis, promote backtracking, compete for substrate GTP, inhibit GTP synthesis, or uncouple transcription-translation by inhibiting translation. Using a combination of cryo-EM, biochemical assays, and quantitative nascent elongating transcript sequencing (qNET-seq), we establish that (p)ppGpp allosterically regulates pausing and nucleotide addition via distinct motions of the RNAP swivel module and both competes with and lowers GTP in vivo. (p)ppGpp stimulates swiveling at pause sites to delay escape but may also inhibit counter-swiveling required in every round of nucleotide addition. PubMed: 42182161DOI: 10.64898/2026.05.13.724835 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.8 Å) |
Structure validation
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