8TOE
Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter
Summary for 8TOE
| Entry DOI | 10.2210/pdb8toe/pdb |
| EMDB information | 41448 |
| Descriptor | DNA-directed RNA polymerase subunit alpha, ZINC ION, DNA-directed RNA polymerase subunit beta, ... (10 entities in total) |
| Functional Keywords | dna-dependent rna polymerase, transcription, intermediate, dna promoter, dna unwinding, transcription-dna complex, transcription/dna |
| Biological source | Escherichia coli (strain K12) More |
| Total number of polymer chains | 9 |
| Total formula weight | 563300.71 |
| Authors | Darst, S.A.,Saecker, R.M.,Mueller, A.U. (deposition date: 2023-08-03, release date: 2024-07-03, Last modification date: 2024-10-23) |
| Primary citation | Saecker, R.M.,Mueller, A.U.,Malone, B.,Chen, J.,Budell, W.C.,Dandey, V.P.,Maruthi, K.,Mendez, J.H.,Molina, N.,Eng, E.T.,Yen, L.Y.,Potter, C.S.,Carragher, B.,Darst, S.A. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat.Struct.Mol.Biol., 2024 Cited by PubMed Abstract: During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAPs), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, here we use time-resolved cryogenic electron microscopy (cryo-EM) to capture four intermediates populated 120 ms or 500 ms after mixing Escherichia coli σ-RNAP and the λP promoter. Cryo-EM snapshots revealed that the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As the nt-strand 'read-out' extends, the RNAP clamp closes, expelling an inhibitory σ domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating that yet unknown conformational changes complete RPo formation in subsequent steps. Given that these events likely describe DNA opening at many bacterial promoters, this study provides insights into how DNA sequence regulates steps of RPo formation. PubMed: 38951624DOI: 10.1038/s41594-024-01349-9 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.9 Å) |
Structure validation
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