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| Title | Assembly landscape for the bacterial large ribosomal subunit. |
|---|---|
| Journal, issue, pages | Nat Commun, Vol. 14, Issue 1, Page 5220, Year 2023 |
| Publish date | Aug 26, 2023 |
 Authors | Kai Sheng / Ning Li / Jessica N Rabuck-Gibbons / Xiyu Dong / Dmitry Lyumkis / James R Williamson /  |
| PubMed Abstract | Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic ...Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic perturbations of the assembly process create bottlenecks where intermediates accumulate, facilitating structural characterization. We use cryo-electron microscopy, with iterative subclassification to identify intermediates in the assembly of the 50S ribosomal subunit from E. coli. The analysis of the ensemble of intermediates that spans the entire biogenesis pathway for the 50 S subunit was facilitated by a dimensionality reduction and cluster picking approach using PCA-UMAP-HDBSCAN. The identity of the cooperative folding units in the RNA with associated proteins is revealed, and the hierarchy of these units reveals a complete assembly map for all RNA and protein components. The assembly generally proceeds co-transcriptionally, with some flexibility in the landscape to ensure efficiency for this central cellular process under a variety of growth conditions. |
 External links | Nat Commun / PubMed:37633970 / PubMed Central |
| Methods | EM (single particle) |
| Resolution | 5.41 - 9.27 Å |
| Structure data |  EMDB-40309: E. coli 50S assembly intermediate from bL17-depletion strain, class: rl17-B-b1  EMDB-40311: E. coli 50S intermediate, bL17-depletion strain, class: rl17-B-b2  EMDB-40313: E. coli 50S intermediate, bL17-depletion strain, class: rl17-B-b3  EMDB-40314: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b1  EMDB-40315: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b2  EMDB-40316: E. coli 50S intermediate, srmB deletion strain, class: srmb-B-a1  EMDB-40317: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b3  EMDB-40318: E. coli 50S intermediate, srmB deletion strain, class: srmb-B-a2  EMDB-40319: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b4  EMDB-40320: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a1  EMDB-40321: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b5  EMDB-40322: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a2  EMDB-40323: E. coli 50S intermediate, bL17-depletion strain, class: rl17-C-b6  EMDB-40324: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a3  EMDB-40325: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a4  EMDB-40327: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-a1  EMDB-40328: E. coli 50S intermediate, srmB deletion strain, class: srmb-C-a5  EMDB-40329: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-a2  EMDB-40330: E. coli 50S intermediate, srmB deletion strain, class: srmb-E-a1  EMDB-40331: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-a3  EMDB-40332: E. coli 50S intermediate, srmB deletion strain, class: srmb-E-a2  EMDB-40333: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-b1  EMDB-40511: E. coli 50S intermediate, bL17-depletion strain, class: rl17-B-b4  EMDB-40512: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-b2  EMDB-40513: E. coli 50S intermediate, srmB deletion strain, class: srmb-E-a3  EMDB-40514: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-b3  EMDB-40515: E. coli 50S intermediate, srmB deletion strain, class: srmb-G1  EMDB-40516: E. coli 50S intermediate, bL17-depletion strain, class: rl17-D-b4  EMDB-40517: E. coli 50S intermediate, srmB deletion strain, class: dead-B-a1  EMDB-40518: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a1  EMDB-40519: E. coli 50S intermediate, srmB deletion strain, class: dead-B-a2  EMDB-40520: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a2  EMDB-40521: E. coli 50S intermediate, srmB deletion strain, class: dead-B-a3  EMDB-40523: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a3  EMDB-40524: E. coli 50S intermediate, deaD deletion strain, class: dead-B-a4  EMDB-40525: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a4  EMDB-40526: E. coli 50S intermediate, deaD deletion strain, class: dead-B-a5  EMDB-40527: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-a5  EMDB-40528: E. coli 50S intermediate, deaD deletion strain, class: dead-B-a6  EMDB-40529: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b1  EMDB-40530: E. coli 50S intermediate, deaD deletion strain, class: dead-B-b1  EMDB-40531: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b10  EMDB-40532: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a1  EMDB-40533: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b2  EMDB-40534: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a2  EMDB-40535: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b3  EMDB-40536: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a3  EMDB-40537: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b4  EMDB-40538: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a4  EMDB-40539: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b5  EMDB-40540: E. coli 50S intermediate, deaD deletion strain, class: dead-C-a5  EMDB-40541: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b6  EMDB-40542: E. coli 50S intermediate, deaD deletion strain, class: dead-C-b1  EMDB-40543: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b7  EMDB-40544: E. coli 50S intermediate, deaD deletion strain, class: dead-C-b2  EMDB-40545: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b8  EMDB-40546: E. coli 50S intermediate, deaD deletion strain, class: dead-E-a1  EMDB-40547: E. coli 50S intermediate, bL17-depletion strain, class: rl17-E-b9  EMDB-40548: E. coli 50S intermediate, deaD deletion strain, class: dead-G1  EMDB-40549: E. coli 50S intermediate, deaD deletion strain, class: dead-preB2  EMDB-40550: E. coli 50S intermediate, deaD deletion strain, class: dead-G2  EMDB-40551: E. coli 50S intermediate, deaD deletion strain, class: dead-preB1  EMDB-40552: E. coli 50S intermediate, deaD deletion strain, class: dead-G3  EMDB-40555: E. coli 50S intermediate, deaD deletion strain, class: dead-G4 |
| Source |
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Escherichia coli K-12 (bacteria)