The EM maps have been deposited in EMDB with the accession numbers EMD-19195, EMD-19196, EMD-19197, EMD-19198, 19199, EMD-19200, EMD-19201, EMD-19202, EMD-19203, and EMD-19204. The molecular models have been deposited in the PDB with accession numbers 8RJB, 8RJC, and 8RJD. The AlphaFold2-predicted structures (Varadi et al., 2024) reported in this study have been deposited in ModelArchive with accession numbers ma-jjnuw, ma-hbsof, ma-hknzh, ma-x3uvj, ma-j8wag, ma-9gsmk, ma-l9qqq, and ma-ise4t.
The following datasets were generated:
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19195. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4. https://www.ebi.ac.uk/emdb/EMD-19195
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19196. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61, all-particle reconstruction. https://www.ebi.ac.uk/emdb/EMD-19196
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19197. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1. https://www.ebi.ac.uk/emdb/EMD-19197
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19198. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2. https://www.ebi.ac.uk/emdb/EMD-19198
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19199. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61, bound TRAP-alpha TMD. https://www.ebi.ac.uk/emdb/EMD-19199
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19200. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, conformation 1. https://www.ebi.ac.uk/emdb/EMD-19200
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19201. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, conformation 2. https://www.ebi.ac.uk/emdb/EMD-19201
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19202. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61, closed conformation 1. https://www.ebi.ac.uk/emdb/EMD-19202
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19203. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61, closed conformation 2. https://www.ebi.ac.uk/emdb/EMD-19203
Lewis AJO Hegde RS (2024) Electron Microscopy Data Bank ID EMD-19204. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Rho-bound Sec61. https://www.ebi.ac.uk/emdb/EMD-19204
Lewis AJO Hegde RS (2024) RCSB Protein Data Bank ID 8RJB. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4. https://www.rcsb.org/structure/8RJB
Lewis AJO Hegde RS (2024) RCSB Protein Data Bank ID 8RJC. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1. https://www.rcsb.org/structure/8RJC
Lewis AJO Hegde RS (2024) RCSB Protein Data Bank ID 8RJD. Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2. https://www.rcsb.org/structure/8RJD
Lewis AJO Hegde RS (2024) ModelArchive ID ma-jjnuw. Chlamydomonas reinhardtii Sec61-RAMP4 complex. https://modelarchive.org/doi/10.5452/ma-jjnuw
Lewis AJO Hedge RS (2024) ModelArchive ID ma-hbsof. Saccharomyces cerevisiae Sec61-RAMP4 complex (aka Ysy6p). https://modelarchive.org/doi/10.5452/ma-hbsof
Lewis AJO Hegde RS (2024) ModelArchive ID ma-hknzh. Canis lupus familiaris Sec61-RAMP4 complex. https://modelarchive.org/doi/10.5452/ma-hknzh
Lewis AJO Hegde RS (2024) ModelArchive ID ma-x3uvj. Heimdallarchaean TRAPα-SecY complex. https://modelarchive.org/doi/10.5452/ma-x3uvj
Lewis AJO Hegde RS (2024) ModelArchive ID ma-j8wag. Trypanosoma brucei TRAP-Sec61 complex. https://modelarchive.org/doi/10.5452/ma-j8wag
Lewis AJO Hegde RS (2024) ModelArchive ID ma-9gsmk. Chlamydomonas reinhardtii TRAP-Sec61-RAMP4-eL38 complex. https://modelarchive.org/doi/10.5452/ma-9gsmk
Lewis AJO Hegde RS (2024) ModelArchive ID ma-l9qqq. Saccharomyces cerevisiae Sec61-TRAP complex (aka Irc22p). https://modelarchive.org/doi/10.5452/ma-l9qqq
Lewis AJO Hegde RS (2024) ModelArchive ID ma-ise4t. Canis lupus familiaris BOS complex (TMEM147/Nicalin/NOMO, C. lupus familiaris). https://modelarchive.org/doi/10.5452/ma-ise4t
The following previously published data sets were used:
Tesina P Ebine S Buschauer R Thoms M Matsuo Y Inada T Beckmann R (2023) RCSB Protein Data Bank ID 8AGX. Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control. https://www.rcsb.org/structure/8AGX
Smirnova J Loerke J Kleinau G Schmidt A Bürger J Meyer EH Mielke T Scheerer P Bock R Spahn CMT Zoschke R (2023) RCSB Protein Data Bank ID 8B2L. Structure of the actively translating plant 80S ribosome at 2.2 Å resolution. https://www.rcsb.org/structure/8B2L
Braunger K Pfeffer S Shrimal S Gilmore R Berninghausen O Mandon EC Becker T Förster F Beckmann R (2018) RCSB Protein Data Bank ID 6FTI. Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum. https://www.rcsb.org/structure/6FTI
Holm M Natchiar SK Rundlet EJ Myasnikov AG Watson ZL Altman RB Wang HY Taunton J Blanchard SC (2023) RCSB Protein Data Bank ID 8GLP. mRNA decoding in human is kinetically and structurally distinct from bacteria. https://www.rcsb.org/structure/8GLP
Holm M Natchiar SK Rundlet EJ Myasnikov AG Watson ZL Altman RB Wang HY Taunton J Blanchard SC (2023) EMDB ID EMD-40205. mRNA decoding in human is kinetically and structurally distinct from bacteria. https://www.ebi.ac.uk/emdb/EMD-40205
Pfeffer S Dudek J Schaffer M Ng BG Albert S Plitzko JM Baumeister W Zimmermann R Freeze HH Engel BD Forster F (2017) EMDB ID EMD-4145. Dissecting the molecular organization of the translocon-associated protein complex. https://www.ebi.ac.uk/emdb/EMD-4145
Braunger K Pfeffer S Shrimal S Gilmore R Berninghausen O Mandon EC Becker T Forster F Beckmann R (2018) EMDB ID EMD-4311. Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum. https://www.ebi.ac.uk/emdb/EMD-4311
Voorhees RM Hegde RS (2016) RCSB Protein Data Bank ID 3JC2. The structure of the mammalian Sec61 channel opened by a signal sequence. https://www.rcsb.org/structure/3JC2
Voorhees RM Hegde RS (2016) EMDB ID EMD-3245. The structure of the mammalian Sec61 channel opened by a signal sequence. https://www.ebi.ac.uk/emdb/EMD-3245
Smalinskaitė L Kim MK Lewis AJO Keenan RJHegde RS (2022) RCSB Protein Data Bank ID 7TM3. Mechanism of an intramembrane chaperone for multipass membrane proteins. https://www.rcsb.org/structure/7TM3
Smalinskaite L Kim MK Lewis AJO Keenan RJHegde RS (2022) EMDB ID EMD-25994. Mechanism of an intramembrane chaperone for multipass membrane proteins. https://www.ebi.ac.uk/emdb/EMD-25994
Gemmer M Chaillet M Lvan Loenhout J (2023) EMDB ID EMD-15885. Visualization of translation and protein biogenesis at the ER membrane. https://www.ebi.ac.uk/emdb/EMD-15885
Gemmer M Chaillet M Lvan Loenhout J (2023) EMDB ID EMD-15889. Visualization of translation and protein biogenesis at the ER membrane. https://www.ebi.ac.uk/emdb/EMD-15889
Gemmer M Fedry JMM Forster FG (2022) RCSB Protein Data Bank ID 8B6L. Subtomogram average of the human Sec61-TRAP-OSTA-translocon. https://www.rcsb.org/structure/8B6L
Gemmer M Fedry JMM Forster FG (2022) EMDB ID EMD-15870. Subtomogram average of the human Sec61-TRAP-OSTA-translocon. https://www.ebi.ac.uk/emdb/EMD-15870
