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Zhong, Frank : University of Chicago
Keenan, Robert J. : University of Chicago : (https://orcid.org/0000-0003-1466-0889)
Hegde, Ramanujan S. : MRC Laboratory of Molecular Biology : (https://orcid.org/0000-0001-8338-852X)
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
National Institutes of Health, R35 GM145374
National Institutes of Health, T32 GM007183
© 2024, Lewis et al.
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
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