Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
Open accessAbstract
The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome-lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane.
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The Sec translocon in bacteria and eukaryotes is organized as a highly modular protein complex and multiple different entities have been structurally and biochemically characterized.
“The Sec translocon in bacteria and eukaryotes is organized as a highly modular protein complex and multiple different entities have been structurally and biochemically characterized (Zimmer et al., 2008; Boy and Koch, 2009; Frauenfeld et al., 2011; Denks et al., 2014; Komar et al., 2016; Kater et al., 2019).”
From The Dynamic SecYEG Translocon (2021) · cites this paper as Frauenfeld et al., 2011
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Self-citationMolecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
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“…discovery of some of the most complicated structures in modern day structural biology (Hsin et al., 2009; Sener et al., 2009; Gumbart et al., 2011; Frauenfeld et al., 2011; Zhao et al., 2013;Wickles et al., 2014). cMDFF and ReMDFF, the new variants of MDFF introduced above, offer now accurate…”
InfluentialSelf-citationStructure of the mammalian oligosaccharyl-transferase complex in the native ER protein translocon
Pfeffer, S., Dudek, J., Gogala, M., Schorr, S., Linxweiler, J., Lang, S., Becker, T. A., Beckmann, R., Zimmermann, R., & Förster, F. G. (2014) · Nature Communications · doi:10.1038/ncomms4072 · Cited by 146 · see citing works
Self-citationArenz, S., Ramu, H., Gupta, P., Berninghausen, O., Beckmann, R., Vázquez‐Laslop, N., Mankin, A. S., & Wilson, D. N. (2014) · Nature Communications · doi:10.1038/ncomms4501 · Cited by 142 · see citing works
Self-citationShen, H., Lithgow, T. J., & Martin, L. L. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms14011589 · Cited by 124 · see citing works
“It allows the SecYEG complex to be investigated in a natural lipid bilayer environment and identifies the ribosome-lipid interactions.”
Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon
Jomaa, A., Boehringer, D., Leibundgut, M., & Ban, N. (2016) · Nature Communications · doi:10.1038/ncomms10471 · Cited by 115 · see citing works
Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography
Wang, X., Xu, F. T., Liu, J., Gao, B., Liu, Y., Zhai, Y., Ma, J., Zhang, K., Baker, T. S., Schulten, K. J., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003132 · Cited by 110 · see citing works
Self-citationConti, B. J., Devaraneni, P. K., Yang, Z., David, L. L., & Skach, W. R. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.018 · Cited by 109 · see citing works
“polypeptidemovement into the lumen versus cytosol (Frauenfeld et al., 2011; Pfeffer et al., 2014).”
Sachelaru, I., Petriman, N.-A., Kudva, R., Kuhn, P., Welte, T., Knapp, B. L., Drepper, F., Warscheid, B., & Koch, H. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.446583 · Cited by 105 · see citing works
The Sec System: Protein Export in Escherichia coli
Crane, J. M., & Randall, L. (2017) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0002-2017 · Cited by 92 · see citing works
Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs
Matthies, D., Bae, C., Toombes, G. E. S., Fox, T. L., Bartesaghi, A., Subramaniam, S., & Swartz, K. J. (2018) · eLife · doi:10.7554/elife.37558 · Cited by 106 · see citing works
Coping with stress: How bacteria fine-tune protein synthesis and protein transport
Njenga, R. K., Boele, J., Öztürk, Y., & Koch, H. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105163 · Cited by 107 · see citing works
Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion
Ulmschneider, M. B., Ulmschneider, J. P., Schiller, N., Wallace, B. A., von HEIJNE, G., & White, S. H. (2014) · Nature Communications · doi:10.1038/ncomms5863 · Cited by 102 · see citing works
Oswald, J., Njenga, R., Natriashvili, A., Sarmah, P., & Koch, H.-G. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.664241 · Cited by 88 · see citing works
Hydrophobicity scales: a thermodynamic looking glass into lipid–protein interactions
MacCallum, J. L., & Tieleman, D. P. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.08.003 · Cited by 94 · see citing works
Structure and 3D Arrangement of Endoplasmic Reticulum Membrane-Associated Ribosomes
Pfeffer, S., Brandt, F., Hrabe, T., Lang, S., Eibauer, M., Zimmermann, R., & Förster, F. G. (2012) · Structure · doi:10.1016/j.str.2012.06.010 · Cited by 94 · see citing works
Welte, T., Kudva, R., Kuhn, P., Sturm, L., Braig, D., Müller, M., Warscheid, B., Drepper, F., & Koch, H.-G. (2012) · Molecular Biology of the Cell · doi:10.1091/mbc.e11-07-0590 · Cited by 87 · see citing works
“These in vitro data suggest that the SRP pathway delivers membrane proteins cotranslationally to two distinct integration sites at the E. coli membrane.”
The Hyaluronan Synthase Catalyzes the Synthesis and Membrane Translocation of Hyaluronan
Hubbard, C., McNamara, J. T., Azumaya, C. M., Patel, M. S., & Zimmer, J. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.01.053 · Cited by 90 · see citing works
Membrane mimetic systems in CryoEM: keeping membrane proteins in their native environment
Autzen, H. E., Julius, D. J., & Cheng, Y. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.05.022 · Cited by 91 · see citing works
Folding pathway of an Ig domain is conserved on and off the ribosome
Tian, P., Steward, A., Kudva, R., Su, T., Shilling, P. J., Nickson, A. A., Hollins, J. J., Beckmann, R., von HEIJNE, G., Clarke, J., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810523115 · Cited by 90 · see citing works
“The ribosomal surface proteins uL23 and uL29 have been suggested to form a potential interaction site for nascent proteins such as trigger factor (44), signal recognition particle (45), and SecYE (46).”
Self-citationMechanisms of ribosome stalling by SecM at multiple elongation steps
Zhang, J., Pan, X., Yan, K., Sun, S., Gao, N., & Sui, S. (2015) · eLife · doi:10.7554/elife.09684 · Cited by 88 · see citing works
“It should be noted that, similar as previous studies of ribosome stalling (Bhushan et al., 2011; Frauenfeld et al., 2011; Halic et al., 2006; Yap and Bernstein, 2009), chloramphenicol was added to maximally preserve the RNC during sample preparation.”
Zhang, M., Huang, R., Ackermann, R., Im, S., Waskell, L. A., Schwendeman, A. A., & Ramamoorthy, A. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201600073 · Cited by 89 · see citing works
Recent advances in nanodisc technology for membrane protein studies (2012–2017)
Rouck, J. E., Krapf, J. E., Roy, J., Huff, H. C., & Das, A. (2017) · FEBS Letters · doi:10.1002/1873-3468.12706 · Cited by 89 · see citing works
Mechanisms of SecM-Mediated Stalling in the Ribosome
Gumbart, J. C., Schreiner, E., Wilson, D. N., Beckmann, R., & Schulten, K. J. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.06.005 · Cited by 86 · see citing works
Self-citationAdvances in the molecular dynamics flexible fitting method for cryo-EM modeling
McGreevy, R., Teo, I., Singharoy, A., & Schulten, K. J. (2016) · Methods · doi:10.1016/j.ymeth.2016.01.009 · Cited by 84 · see citing works
“The present article concerns MDFF, which has proven to be successful in the hands of its developers as evidenced by applications to solving structural models for the ribosome [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30], photosynthetic proteins [31, 32], myosin [33], chaperonins [29], bacterial chemosensory ar…”
Self-citationSingle particle electron cryo-microscopy of a mammalian ion channel
Liao, M., Cao, E., Julius, D. J., & Cheng, Y. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.02.005 · Cited by 86 · see citing works
A structural model of the active ribosome-bound membrane protein insertase YidC
Wickles, S., Singharoy, A., Andréani, J., Seemayer, S., Bischoff, L., Berninghausen, O., Söding, J., Schulten, K. J., van der Sluis, E. O., & Beckmann, R. (2014) · eLife · doi:10.7554/elife.03035 · Cited by 86 · see citing works
Self-citationBiogenesis of inner membrane proteins in Escherichia coli
Luirink, J., Yu, Z. K., Wagner, S., & Gier, J. D. (2011) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2011.12.006 · Cited by 87 · see citing works
Fidelity of Cotranslational Protein Targeting by the Signal Recognition Particle
Zhang, X., & Shan, S. (2014) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-051013-022653 · Cited by 83 · see citing works
“Because both SecYEG and the SRP NG-domain contact the ribosome via the L23 protein and hence must compete for overlapping binding sites (10, 11, 42, 90), the movement of the GTPase complex away from the ribosome exit (while its M-domain is still bound to the signal sequence) also suggests an attractive mechanism for h…”
Distribution of mechanical stress in the Escherichia coli cell envelope
Hwang, H. J., Paracini, N., Parks, J. M., Lakey, J. H., & Gumbart, J. C. (2018) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2018.09.020 · Cited by 82 · see citing works
Self-citationStructure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches
Jones, A. J. Y., Gabriel, F., Tandale, A., & Nietlispach, D. (2020) · Molecules · doi:10.3390/molecules25204729 · Cited by 81 · see citing works
An allosteric Sec61 inhibitor traps nascent transmembrane helices at the lateral gate
MacKinnon, A. L., Paavilainen, V. O., Sharma, A., Hegde, R. S., & Taunton, J. (2014) · eLife · doi:10.7554/elife.01483 · Cited by 78 · see citing works
“Structural, mutagenesis, and crosslinking analyses have all converged on the lateral gate as the site where hydrophobic segments exit the central pore of Sec61 and enter the lipid bilayer (du Plessis et al., 2009; Egea and Stroud, 2010; Frauenfeld et al., 2011; Plath et al., 1998; Trueman et al., 2011; Tsukazaki et al…”
InfluentialThe E. coli S30 lysate proteome: A prototype for cell-free protein production
Foshag, D., Henrich, E., Hiller, E., Schäfer, M., Kerger, C., Burger‐Kentischer, A., Díaz‐Moreno, I., García‐Mauriño, S. M., Dötsch, V., Rupp, S., et al. (2017) · New Biotechnology · doi:10.1016/j.nbt.2017.09.005 · Cited by 79 · see citing works
Targeting and Insertion of Membrane Proteins
Kühn, A., Koch, H., & Dalbey, R. (2017) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0012-2016 · Cited by 80 · see citing works
“Early crosslinking experiments had shown that a signal sequence of a preprotein binds in the lateral gate (136) and this was verified by cryo-electron microscopy of a nascent “in transloco” complex (137).”
How Does the Ribosome Fold the Proteome?
Cassaignau, A. M. E., Cabrita, L. D., & Christodoulou, J. C. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-062917-012226 · Cited by 73 · see citing works
Reggie, L., Lopez, J. J., Collinson, I. R., Glaubitz, C., & Lorch, M. (2011) · Journal of the American Chemical Society · doi:10.1021/ja209378h · Cited by 74 · see citing works
Efremov, R. G., Gatsogiannis, C., & Raunser, S. (2017) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2017.05.007 · Cited by 75 · see citing works
Co-translational protein targeting to the bacterial membrane
Saraogi, I., & Shan, S. (2013) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2013.10.013 · Cited by 74 · see citing works
Breaking on through to the other side: protein export through the bacterial Sec system
Chatzi, K. E., Sardis, M. F., Spyridoula Karamanou, A., & Economou, A. (2012) · Biochemical Journal · doi:10.1042/bj20121227 · Cited by 74 · see citing works
Dynamics of co-translational protein targeting
Elvekrog, M., & Walter, P. (2015) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2015.09.016 · Cited by 71 · see citing works
“Cryo-EM reconstructions of SRP-RNC complexes [47– 49] and RNC-translocon complexes [50 ,51 ,52,53] show that SRP’s binding site on the large ribosomal subunit partially overlaps with the binding site of the translocon with the ribosome.”
Charge-driven dynamics of nascent-chain movement through the SecYEG translocon
Ismail, N., Hedman, R., Lindén, M., & von HEIJNE, G. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2940 · Cited by 72 · see citing works
Hall, S. C. L., Tognoloni, C., Price, G. J., Klumperman, B., Edler, K. J., Dafforn, T. R., & Arnold, T. (2017) · Biomacromolecules · doi:10.1021/acs.biomac.7b01539 · Cited by 72 · see citing works
Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes
Goh, B. C., Hadden‐Perilla, J. A., Bernardi, R. C., Singharoy, A., McGreevy, R., Rudack, T., Cassidy, C. K., & Schulten, K. J. (2016) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062215-011113 · Cited by 69 · see citing works
“…proteins into their native states, and membrane proteins are assisted in their membrane placement by insertases such as YidC (70) and SecY (44, 51) shown in Figure 4a. TF was long thought to bind to the ribosome as a rigid molecule (71, 110); however, recent structures of TF bound to…”
Self-citationStructure of the SecY complex unlocked by a preprotein mimic.
Hizlan, D., Robson, A., Whitehouse, S., Gold, V. A., Vonck, J., Mills, D., Kühlbrandt, W., & Collinson, I. (2012) · Cell Reports · doi:10.1016/j.celrep.2011.11.003 · Cited by 68 · see citing works
“The SecYEG-ribosome complex in the act of cotranslational transport of a membrane protein has also been visualized in a lipid bilayer, in this case encapsulated by nanodiscs (Frauenfeld et al., 2011).”
InfluentialThe largely unexplored biology of small proteins in pro‐ and eukaryotes
Steinberg, R., & Koch, H. (2021) · FEBS Journal · doi:10.1111/febs.15845 · Cited by 71 · see citing works
Visualization of a polytopic membrane protein during SecY-mediated membrane insertion
Bischoff, L., Wickles, S., Berninghausen, O., van der Sluis, E. O., & Beckmann, R. (2014) · Nature Communications · doi:10.1038/ncomms5103 · Cited by 69 · see citing works
Self-citationTanaka, Y., Sugano, Y., Takemoto, M., Mori, T., Furukawa, A., Kusakizako, T., Kumazaki, K., Kashima, A., Ishitani, R., Sugita, Y., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.10.025 · Cited by 68 · see citing works
“During protein translocation and insertion, conformational changes in SecYEG are induced by interactions between preproteins and their cytosolic partners, such as SecA and the ribosome (Bischoff et al., 2014; Frauenfeld et al., 2011; Gogala et al., 2014; Park et al., 2014; Zimmer et al., 2008).”
Bengtsen, T., Holm-Janas, V., Kjølbye, L. R., Midtgaard, S. R., Johansen, N. T., Tesei, G., Bottaro, S., Schiøtt, B., Arleth, L., & Lindorff‐Larsen, K. (2020) · eLife · doi:10.7554/elife.56518 · Cited by 68 · see citing works
“Negative stain transmission electron microscopy of Δ H4H5 appears to show discs of different shapes ( Bibow et al., 2017 ), whereas class-averaged cryo-electron microscopy of a membrane protein embedded in a different nanodisc appears more symmetric ( Frauenfeld et al., 2011 ).”
Symmetry-Restrained Flexible Fitting for Symmetric EM Maps
Chan, K., Gumbart, J. C., McGreevy, R., Watermeyer, J. M., Sewell, B. T., & Schulten, K. J. (2011) · Structure · doi:10.1016/j.str.2011.07.017 · Cited by 68 · see citing works
“Structure 19, 1211–12 (Agirrezabala et al., 2008; Frauenfeld et al., 2011; Qian et al., 2005; Seidelt et al., 2009; Zhang et al., 2010b).”
Self-citationKynde, S., Skar‐Gislinge, N., Pedersen, M. C., Midtgaard, S. R., Simonsen, J. B., Schweins, R., Mortensen, K., & Arleth, L. (2014) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s1399004713028344 · Cited by 67 · see citing works
“Interesting results have already been obtained using cryo-EM on a membrane-anchored protein system (Frauenfeld et al., 2011), and the nanodisc platform was recently used in a very interesting NMR study of fully embedded transmembrane structures (Hagn et al., 2013).”
Jomaa, A., Fu, Y.-H. H., Boehringer, D., Leibundgut, M., Shan, S.-O., & Ban, N. (2017) · Nature Communications · doi:10.1038/ncomms15470 · Cited by 66 · see citing works
Bocquet, N., Kohler, J., Hug, M. N., Kusznir, E. A., Rufer, A. C., Dawson, R. J. P., Hennig, M., Ruf, A., Huber, W., & Huber, S. (2015) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2015.02.014 · Cited by 66 · see citing works
“PDB accession codes used to generate themodels: A2A, pdb: 3REY from the reference [27], the nanodiscmodel has been extracted from pdb 3JOO in reference [28] and the eGFP from pdb 2YOG from reference [29].”
Dominik, P. K., Borowska, M. T., Dalmas, O., Kim, S. S., Perozo, E., Keenan, R. J., & Kossiakoff, A. A. (2015) · Structure · doi:10.1016/j.str.2015.11.014 · Cited by 64 · see citing works
“In addition, the technology to collect EM data on nanodisc-embedded targets is being further developed and offers the opportunity to quickly provide microscopists ready-made systems with customized fiducial markers (Frauenfeld et al., 2011; Wu et al., 2012; Choi et al., 2013; Gogol et al., 2013).”
Cryo‐Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method
Chan, K., Trabuco, L. G., Schreiner, E., & Schulten, K. J. (2012) · Biopolymers · doi:10.1002/bip.22042 · Cited by 65 · see citing works
Self-citationDetecting pore-lining regions in transmembrane protein sequences
Nugent, T., & Jones, D. T. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-169 · Cited by 63 · see citing works
“Aside from ions and small molecules, other channels and transporters mediate the transfer of a range of larger biological molecules across the membrane including proteins by the general secretory pathway (SEC) translocase family [7], double-stranded DNA by the septal DNA translocator (S-DNA-T) family [8-10] and mRNA v…”
Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion
Ge, Y., Draycheva, A., Bornemann, T., Rodnina, M. V., & Wintermeyer, W. (2014) · Nature Communications · doi:10.1038/ncomms6263 · Cited by 60 · see citing works
Competitive Binding of the SecA ATPase and Ribosomes to the SecYEG Translocon
Wu, Z. C., de Keyzer, J., Kedrov, A., & Driessen, A. J. M. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.297911 · Cited by 58 · see citing works
“However, the overlapping binding sites (7, 8, 10) and the anticipated steric constraints upon association of these two large ligands make this difficult to envision.”
InfluentialExploring the Antimicrobial Action of Quaternary Amines against Acinetobacter baumannii
Knauf, G. A., Cunningham, A. L., Kazi, M. I., Riddington, I. M., Crofts, A. A., Cattoir, V., Trent, M. S., & Davies, B. W. (2018) · mBio · doi:10.1128/mbio.02394-17 · Cited by 61 · see citing works
“Ribosomal proteins L23 and L24 are located together near the exit tunnel and interact with SecY during protein secretion (38), while S11 is a component of the ribosomal P site and interacts with S7 to influence translation fidelity (39) (Fig.”
Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation
Zhang, B., & Miller, T. F. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.039 · Cited by 58 · see citing works
“Extensive structural (Van den Berg et al., 2004; Egea and Stroud, 2011; Frauenfeld et al., 2011; Tsukazaki et al., 2008; Zimmer et al., 2008), biochemical (Bonardi et al.”
Structural Dynamics of the YidC:Ribosome Complex during Membrane Protein Biogenesis
Kedrov, A., Wickles, S., Crevenna, Á. H., van der Sluis, E. O., Buschauer, R., Berninghausen, O., Lamb, D. C., & Beckmann, R. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.11.059 · Cited by 57 · see citing works
“Although several membrane proteins have been meanwhile visualized by cryo-EM in a near physiological lipid environment (Frauenfeld et al., 2011; Efremov et al., 2015; Gao et al., 2016), better structural analysis of YidC:ribosome complex has been hindered by the small size of the insertase (functional core 30 kDa), by…”
Self-citationYidC and SecYEG form a heterotetrameric protein translocation channel.
Sachelaru, I., Winter, L., Knyazev, D. G., Zimmermann, M., Vogt, A., Kuttner, R., Ollinger, N., Siligan, C., Pohl, P., & Koch, H.-G. (2017) · Scientific Reports · doi:10.1038/s41598-017-00109-8 · Cited by 58 · see citing works
Membrane protein structures without crystals, by single particle electron cryomicroscopy
Vinothkumar, K. R. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.07.009 · Cited by 58 · see citing works
Lipid Internal Dynamics Probed in Nanodiscs
Martinez, D., Décossas, M., Kowal, J., Frey, L., Stahlberg, H., Dufourc, É. J., Riek, R., Habenstein, B., Bibow, S., & Loquet, A. (2017) · ChemPhysChem · doi:10.1002/cphc.201700450 · Cited by 58 · see citing works
Nanodiscs in the Studies of Membrane-Bound Cytochrome P450 Enzymes
Luthra, A., Gregory, M. C., Grinkova, Y. V., Denisov, I. G., & Sligar, S. G. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-321-3_10 · Cited by 58 · see citing works
“Since its development, the Nanodisc technology has proved to be the method of choice for detailed mechanistic studies of G-protein-coupled receptor systems [21-26], cytochromes P450 [16, 20, 27-37], ion channels [38-41], transporters [42-47], chemotactic receptors [48-49], and other biological systems [50-53].”
SecYEG activates GTPases to drive the completion of cotranslational protein targeting
Akopian, D., Dalal, K., Shen, K., Duong, F., & Shan, S. (2013) · The Journal of Cell Biology · doi:10.1083/jcb.201208045 · Cited by 56 · see citing works
Molecular landscape of etioplast inner membranes in higher plants
Floris, D., & Kühlbrandt, W. (2021) · Nature Plants · doi:10.1038/s41477-021-00896-z · Cited by 56 · see citing works
Skar‐Gislinge, N., Kynde, S., Denisov, I. G., Ye, X., Lenov, I. L., Sligar, S. G., & Arleth, L. (2015) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s1399004715018702 · Cited by 55 · see citing works
“It is our hope that the use of the nanodisc system and SAS, in conjunction with complementary structural techniques such as cryo-EM (Frauenfeld et al., 2011) and NMR (Hagn et al., 2013), will be able to accelerate studies of membrane proteins that have previously been inaccessible to structural…”
Modulating co-translational protein folding by rational design and ribosome engineering
Ahn, M., Włodarski, T., Mitropoulou, A., Chan, S. H. S., Sidhu, H., Plessa, E., Becker, T. A., Budisa, N., Waudby, C. A., Beckmann, R., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31906-z · Cited by 45 · see citing works
“Within the tunnel, the loops create an irregular trajectory for the NC by partially occluding the upper (uL4 and uL22 at the constriction) and lower (uL23 and uL24) parts of the tunnel, and thus force direct contacts to be made with emerging NCs 18 (Fig.”
Self-citationProtein transport across the bacterial plasma membrane by the sec pathway.
Smets, D., Loos, M. S., Karamanou, S., & Economou, A. (2019) · The Protein Journal · doi:10.1007/s10930-019-09841-8 · Cited by 48 · see citing works
Lipids Activate SecA for High Affinity Binding to the SecYEG Complex
Koch, S., de Wit, J. G., Vos, I., Birkner, J. P., Gordiichuk, P. I., Herrmann, A. P., van Oijen, A. M., & Driessen, A. J. M. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.743831 · Cited by 53 · see citing works
“According to the dimensions of SecYEG, 20% of the small discs will be occupied by the translocation complex, leaving only a low lipid surface area unoccupied (26).”
Eibauer, M., Hoffmann, C., Plitzko, J. M., Baumeister, W. P., Nickell, S., & Engelhardt, H. (2012) · Journal of Structural Biology · doi:10.1016/j.jsb.2012.09.008 · Cited by 51 · see citing works
“, 2000; Frank, 2006; Grigorieff, 2007), allowing to generate 3D reconstructions in the subnanometer range (e.g. Booth et al., 2004; Bohn et al., 2010; Frauenfeld et al., 2011), due to practical reasons CTF correction is currently not routinely applied in cryo-electron tomography.”
Memtein: The fundamental unit of membrane-protein structure and function
Overduin, M., & Esmaili, M. (2018) · Chemistry and Physics of Lipids · doi:10.1016/j.chemphyslip.2018.11.008 · Cited by 52 · see citing works
Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations
Gumbart, J. C., & Roux, B. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.01.021 · Cited by 51 · see citing works
“Membrane insertion of a TM segment in the cotranslational system is believed to occur via a two-stage process, the first being insertion from ribosome into the channel and the second from the channel laterally into the membrane (15,17).”
Self-citationStructure and Dynamics of Phospholipid Nanodiscs from All-Atom and Coarse-Grained Simulations
Debnath, A., & Schäfer, L. V. (2015) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5b02101 · Cited by 51 · see citing works
Partially inserted nascent chain unzips the lateral gate of the Sec translocon.
Kater, L., Frieg, B., Berninghausen, O., Gohlke, H., Beckmann, R., & Kedrov, A. (2019) · The EMBO Reports · doi:10.15252/embr.201948191 · Cited by 43 · see citing works
“No SecG subunit could be resolved in the earlier structure of SecYEG-ND [14], and the crystal structure of the quiescent SecYEG revealed that SecG TMH 1 faces away from the translocon core, so its periplasmic tip is separated by ~10 Å from the nearest TMH 4 of SecY, with a”
InfluentialSelf-citationxMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures
McGreevy, R., Singharoy, A., Li, Q., Zhang, J., Xu, D. H., Perozo, E., & Schulten, K. J. (2014) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s1399004714013856 · Cited by 49 · see citing works
“Additionally, membrane proteins can be simulated in a membrane, as in the previous case of MDFF studies of the ribosome (Frauenfeld et al., 2011).”
Self-citationBacterial protein translocation requires only one copy of the SecY complex in vivo
Park, E., & Rapoport, T. A. (2012) · The Journal of Cell Biology · doi:10.1083/jcb.201205140 · Cited by 48 · see citing works
“After quenching with 20 mM -mercaptoethanol for 20 min at 4°C, the cells were washed three times with 1 mL of the buffer and then resuspended in 200 μl SecY channel in such a way that a nascent polypeptide can move directly from the ribosome tunnel into the SecY channel (Ménétret et al., 2007, 2008; Becker et al., 20…”
InfluentialLipid environment of membrane proteins in cryo-EM based structural analysis
Mio, K., & Sato, C. (2017) · Biophysical Reviews · doi:10.1007/s12551-017-0371-6 · Cited by 48 · see citing works
“(Frauenfeld et al. 2011), ribosome–YidC complex (Kedrov et al.”
- Authors
- Frauenfeld, J., Gumbart, J., Sluis, E. O. V. D., Funes, S., Gartmann, M., Beatrix, B., Mielke, T., Berninghausen, O., Becker, T., Schulten, K., & Beckmann, R.
- Affiliations
- Ludwig-Maximilians-Universität München (DE)
- University of Illinois Urbana-Champaign (US)
- Center for Integrated Protein Science Munich (DE)
- Universidad Nacional Autónoma de México (MX)
- Max Planck Institute for Molecular Genetics (DE)
- Corresponding author
- Beckmann, Roland
- ORCID
- Venue
- Nature Structural & Molecular Biology
- Published
- 2011-04-17
- Volume
- 18
- Issue
- 5
- Pages
- 614-621
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC3412285
- OpenAlex
- W2117213358
- Cited by
- 298
- References
- 63
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 12 · 2023: 4 · 2022: 12 · 2021: 12 · 2020: 18 · 2019: 23 · 2018: 26 · 2017: 23 · 2016: 26 · 2015: 33 · 2014: 26 · 2013: 31 · 2012: 29
- FWCI
- 12.87
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Boehringer Ingelheim Fonds
- National Institute of General Medical Sciences (R01GM067887)
- National Center for Research Resources (P41RR005969)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Keywords
- protein translocation, membrane insertion, protein-conducting channel, lateral gate, peptidyl transferase center, nascent polypeptide chains, nanodisc reconstitution, membrane environment
- MeSH terms
- SEC Translocation Channels, Cell Membrane, Escherichia coli, Lipoproteins, HDL, Membrane Proteins, Models, Molecular, Ribosomes, Signal Recognition Particle, Cryoelectron Microscopy, Protein Transport, Escherichia coli Proteins
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