EMD-19198
Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2
EMD-19198
Single-particle2.78574 Å
Deposition: 20/12/2023
Map released: 24/01/2024
Last modified: 13/11/2024
Sample Organism:
Oryctolagus cuniculus,
Canis lupus familiaris,
Oryctolagus,
Bos taurus,
Sus scrofa
Sample: 80S ribosome translating a stalled, two-TMD nascent chain (derived from rhodopsin), and bound to Sec61, the TRAP complex, and RAMP4
Fitted models: 8rjd (Avg. Q-score: 0.573)
Deposition Authors: Lewis AJO , Hegde RS
Sample: 80S ribosome translating a stalled, two-TMD nascent chain (derived from rhodopsin), and bound to Sec61, the TRAP complex, and RAMP4
Fitted models: 8rjd (Avg. Q-score: 0.573)
Deposition Authors: Lewis AJO , Hegde RS
Structural analysis of the dynamic ribosome-translocon complex.
Abstract:
The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.
The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.
Secondary citations:
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- & Croll TI. (2018) ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol, 74, 519 - 530
- Kimanius D, Dong L, Sharov G, Nakane T & Scheres SHW. (2021) New tools for automated cryo-EM single-particle analysis in RELION-4.0. 478, 4169 - 4185