Structural Basis of the Sec Translocon and YidC Revealed Through X-ray Crystallography

  • Tomoya TsukazakiEmail author


Protein translocation and membrane integration are fundamental, conserved processes. After or during ribosomal protein synthesis, precursor proteins containing an N-terminal signal sequence are directed to a conserved membrane protein complex called the Sec translocon (also known as the Sec translocase) in the endoplasmic reticulum membrane in eukaryotic cells, or the cytoplasmic membrane in bacteria. The Sec translocon comprises the Sec61 complex in eukaryotic cells, or the SecY complex in bacteria, and mediates translocation of substrate proteins across/into the membrane. Several membrane proteins are associated with the Sec translocon. In Escherichia coli, the membrane protein YidC functions not only as a chaperone for membrane protein biogenesis along with the Sec translocon, but also as an independent membrane protein insertase. To understand the molecular mechanism underlying these dynamic processes at the membrane, high-resolution structural models of these proteins are needed. This review focuses on X-ray crystallographic analyses of the Sec translocon and YidC and discusses the structural basis for protein translocation and integration.


Protein translocation Protein insertion X-ray crystallography Membrane protein Sec translocon 



I thank K. Abe for providing secretarial assistance. This review was supported by the JSPS/MEXT KAKENHI (Grant Nos. JP26119007, JP18H02405, and JP18KK0197).


  1. 1.
    Rapoport TA, Li L, Park E (2017) Structural and mechanistic insights into protein translocation. Annu Rev Cell Dev Biol 33:369–390. CrossRefGoogle Scholar
  2. 2.
    Tsirigotaki A, De Geyter J, Sostaric N, Economou A, Karamanou S (2017) Protein export through the bacterial Sec pathway. Nat Rev Microbiol 15:21–36. CrossRefGoogle Scholar
  3. 3.
    Blobel G, Dobberstein B (1975) Transfer of proteins across membranes. J Cell Biol 67:835–862CrossRefGoogle Scholar
  4. 4.
    Akopian D, Shen K, Zhang X, Shan SO (2013) Signal recognition particle: an essential protein-targeting machine. Annu Rev Biochem 82:693–721. CrossRefGoogle Scholar
  5. 5.
    Matlack KE, Misselwitz B, Plath K, Rapoport TA (1999) BiP acts as a molecular ratchet during posttranslational transport of prepro-α factor across the ER membrane. Cell 97:553–564. CrossRefGoogle Scholar
  6. 6.
    Chatzi KE, Sardis MF, Economou A, Karamanou S (2014) SecA-mediated targeting and translocation of secretory proteins. Biochim Biophys Acta 1843:1466–1474. CrossRefGoogle Scholar
  7. 7.
    Hartl FU, Lecker S, Schiebel E, Hendrick JP, Wickner W (1990) The binding cascade of SecB to SecA to SecY/E mediates preprotein targeting to the E. coli plasma membrane. Cell 63:269–279. CrossRefGoogle Scholar
  8. 8.
    Economou A, Wickner W (1994) SecA promotes preprotein translocation by undergoing ATP-driven cycles of membrane insertion and deinsertion. Cell 78:835–843. CrossRefGoogle Scholar
  9. 9.
    Braunger K et al (2018) Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum. Science 360:215–219. CrossRefGoogle Scholar
  10. 10.
    Pfeffer S et al (2017) Dissecting the molecular organization of the translocon-associated protein complex. Nat Commun 8:14516. CrossRefGoogle Scholar
  11. 11.
    Tsukazaki T (2018) Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor. FEMS Microbiol Lett 365:fny112. CrossRefGoogle Scholar
  12. 12.
    Duong F, Wickner W (1997) Distinct catalytic roles of the SecYE, SecG and SecDFyajC subunits of preprotein translocase holoenzyme. EMBO J 16:2756–2768. CrossRefGoogle Scholar
  13. 13.
    Tsukazaki T et al (2011) Structure and function of a membrane component SecDF that enhances protein export. Nature 474:235–238. CrossRefGoogle Scholar
  14. 14.
    Furukawa A, Nakayama S, Yoshikaie K, Tanaka Y, Tsukazaki T (2018) Remote coupled drastic β-barrel to β-sheet transition of the protein translocation motor. Structure 26:485–489. CrossRefGoogle Scholar
  15. 15.
    Furukawa A et al (2017) Tunnel formation inferred from the I-form structures of the proton-driven protein secretion motor SecDF. Cell Rep 19:895–901. CrossRefGoogle Scholar
  16. 16.
    Kiefer D, Kuhn A (2018) YidC-mediated membrane insertion. FEMS Microbiol Lett 365:fny106. CrossRefGoogle Scholar
  17. 17.
    Hennon SW, Soman R, Zhu L, Dalbey RE (2015) YidC/Alb3/Oxa1 Family of Insertases. J Biol Chem 290:14866–14874. CrossRefGoogle Scholar
  18. 18.
    Nishikawa H, Sasaki M, Nishiyama KI (2017) Membrane insertion of F0 c subunit of F0F1 ATPase depends on glycolipozyme MPIase and is stimulated by YidC. Biochem Biophys Res Commun 487:477–482. CrossRefGoogle Scholar
  19. 19.
    Nishiyama K et al (2012) MPIase is a glycolipozyme essential for membrane protein integration. Nat Commun 3:1260. CrossRefGoogle Scholar
  20. 20.
    Wang P, Dalbey RE (2011) Inserting membrane proteins: the YidC/Oxa1/Alb3 machinery in bacteria, mitochondria, and chloroplasts. Biochim Biophys Acta 1808:866–875. CrossRefGoogle Scholar
  21. 21.
    van den Berg B et al (2004) X-ray structure of a protein-conducting channel. Nature 427:36–44. CrossRefGoogle Scholar
  22. 22.
    du Plessis DJ, Nouwen N, Driessen AJ (2011) The Sec translocase. Biochim Biophys Acta 1808:851–865. CrossRefGoogle Scholar
  23. 23.
    Tsukazaki T et al (2008) Conformational transition of Sec machinery inferred from bacterial SecYE structures. Nature 455:988–991. CrossRefGoogle Scholar
  24. 24.
    Egea PF, Stroud RM (2010) Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes. Proc Natl Acad Sci USA 107:17182–17187. CrossRefGoogle Scholar
  25. 25.
    Zimmer J, Nam Y, Rapoport TA (2008) Structure of a complex of the ATPase SecA and the protein-translocation channel. Nature 455:936–943. CrossRefGoogle Scholar
  26. 26.
    Li L et al (2016) Crystal structure of a substrate-engaged SecY protein-translocation channel. Nature 531:395–399. CrossRefGoogle Scholar
  27. 27.
    Tanaka Y et al (2015) Crystal structures of SecYEG in lipidic cubic phase elucidate a precise resting and a peptide-bound state. Cell Rep 13:1561–1568. CrossRefGoogle Scholar
  28. 28.
    Li W et al (2007) The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal. Mol Cell 26:511–521. CrossRefGoogle Scholar
  29. 29.
    Flower AM, Hines LL, Pfennig PL (2000) SecG is an auxiliary component of the protein export apparatus of Escherichia coli. Mol Gen Genet 263:131–136. CrossRefGoogle Scholar
  30. 30.
    Nishiyama K, Hanada M, Tokuda H (1994) Disruption of the gene encoding p12 (SecG) reveals the direct involvement and important function of SecG in the protein translocation of Escherichia coli at low temperature. EMBO J 13:3272–3277CrossRefGoogle Scholar
  31. 31.
    Bost S, Belin D (1995) A new genetic selection identifies essential residues in SecG, a component of the Escherichia coli protein export machinery. EMBO J 14:4412–4421CrossRefGoogle Scholar
  32. 32.
    Brundage L, Hendrick JP, Schiebel E, Driessen AJ, Wickner W (1990) The purified E. coli integral membrane protein SecY/E is sufficient for reconstitution of SecA-dependent precursor protein translocation. Cell 62:649–657. CrossRefGoogle Scholar
  33. 33.
    Plath K, Mothes W, Wilkinson BM, Stirling CJ, Rapoport TA (1998) Signal sequence recognition in posttranslational protein transport across the yeast ER membrane. Cell 94:795–807. CrossRefGoogle Scholar
  34. 34.
    Tam PC, Maillard AP, Chan KK, Duong F (2005) Investigating the SecY plug movement at the SecYEG translocation channel. EMBO J 24:3380–3388. CrossRefGoogle Scholar
  35. 35.
    Allen WJ et al (2016) Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation. eLife 5:e15598. CrossRefGoogle Scholar
  36. 36.
    Cannon KS, Or E, Clemons WM Jr, Shibata Y, Rapoport TA (2005) Disulfide bridge formation between SecY and a translocating polypeptide localizes the translocation pore to the center of SecY. J Cell Biol 169:219–225. CrossRefGoogle Scholar
  37. 37.
    Ge Y, Draycheva A, Bornemann T, Rodnina MV, Wintermeyer W (2014) Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion. Nat Commun 5:5263. CrossRefGoogle Scholar
  38. 38.
    Bischoff L, Wickles S, Berninghausen O, van der Sluis EO, Beckmann R (2014) Visualization of a polytopic membrane protein during SecY-mediated membrane insertion. Nat Commun 5:4103. CrossRefGoogle Scholar
  39. 39.
    Gogala M et al (2014) Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion. Nature 506:107–110. CrossRefGoogle Scholar
  40. 40.
    Park E et al (2014) Structure of the SecY channel during initiation of protein translocation. Nature 506:102–106. CrossRefGoogle Scholar
  41. 41.
    Voorhees RM, Fernandez IS, Scheres SH, Hegde RS (2014) Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution. Cell 157:1632–1643. CrossRefGoogle Scholar
  42. 42.
    Voorhees RM, Hegde RS (2016) Structure of the Sec61 channel opened by a signal sequence. Science 351:88–91. CrossRefGoogle Scholar
  43. 43.
    Pfeffer S et al (2015) Structure of the native Sec61 protein-conducting channel. Nat Commun 6:8403. CrossRefGoogle Scholar
  44. 44.
    Jomaa A, Boehringer D, Leibundgut M, Ban N (2016) Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon. Nat Commun 7:10471. CrossRefGoogle Scholar
  45. 45.
    Kedrov A, Kusters I, Krasnikov VV, Driessen AJ (2011) A single copy of SecYEG is sufficient for preprotein translocation. EMBO J 30:4387–4397. CrossRefGoogle Scholar
  46. 46.
    Park E, Rapoport TA (2012) Bacterial protein translocation requires only one copy of the SecY complex in vivo. J Cell Biol 198:881–893. CrossRefGoogle Scholar
  47. 47.
    Dalal K, Chan CS, Sligar SG, Duong F (2012) Two copies of the SecY channel and acidic lipids are necessary to activate the SecA translocation ATPase. Proc Natl Acad Sci USA 109:4104–4109. CrossRefGoogle Scholar
  48. 48.
    Osborne AR, Rapoport TA (2007) Protein translocation is mediated by oligomers of the SecY complex with one SecY copy forming the channel. Cell 129:97–110. CrossRefGoogle Scholar
  49. 49.
    Kedrov A et al (2016) Structural dynamics of the YidC: ribosome complex during membrane protein biogenesis. Cell Rep 17:2943–2954. CrossRefGoogle Scholar
  50. 50.
    Tanaka Y et al (2018) 2.8-Å crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop. Biochem Biophys Res Commun 505:141–145. CrossRefGoogle Scholar
  51. 51.
    Kumazaki K et al (2014) Structural basis of Sec-independent membrane protein insertion by YidC. Nature 509:516–520. CrossRefGoogle Scholar
  52. 52.
    Kumazaki K et al (2014) Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase. Sci Rep 4:7299. CrossRefGoogle Scholar
  53. 53.
    Xin Y et al (2018) Structure of YidC from Thermotoga maritima and its implications for YidC-mediated membrane protein insertion. FASEB J 32:2411–2421. CrossRefGoogle Scholar
  54. 54.
    Kedrov A et al (2013) Elucidating the native architecture of the YidC: ribosome complex. J Mol Biol 425:4112–4124. CrossRefGoogle Scholar
  55. 55.
    Wickles S et al (2014) A structural model of the active ribosome-bound membrane protein insertase YidC. elife 3:e03035. CrossRefGoogle Scholar
  56. 56.
    Spann D, Pross E, Chen Y, Dalbey RE, Kuhn A (2018) Each protomer of a dimeric YidC functions as a single membrane insertase. Sci Rep 8:589. CrossRefGoogle Scholar
  57. 57.
    Kohler R et al (2009) YidC and Oxa1 form dimeric insertion pores on the translating ribosome. Mol Cell 34:344–353. CrossRefGoogle Scholar
  58. 58.
    Lotz M, Haase W, Kuhlbrandt W, Collinson I (2008) Projection structure of yidC: a conserved mediator of membrane protein assembly. J Mol Biol 375:901–907. CrossRefGoogle Scholar
  59. 59.
    Petriman NA et al (2018) The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY. Sci Rep 8:578. CrossRefGoogle Scholar
  60. 60.
    Klenner C, Kuhn A (2012) Dynamic disulfide scanning of the membrane-inserting Pf3 coat protein reveals multiple YidC substrate contacts. J Biol Chem 287:3769–3776. CrossRefGoogle Scholar
  61. 61.
    Klenner C, Yuan J, Dalbey RE, Kuhn A (2008) The Pf3 coat protein contacts TM1 and TM3 of YidC during membrane biogenesis. FEBS Lett 582:3967–3972. CrossRefGoogle Scholar
  62. 62.
    Jiang F et al (2003) Defining the regions of Escherichia coli YidC that contribute to activity. J Biol Chem 278:48965–48972. CrossRefGoogle Scholar
  63. 63.
    Xie K, Kiefer D, Nagler G, Dalbey RE, Kuhn A (2006) Different regions of the nonconserved large periplasmic domain of Escherichia coli YidC are involved in the SecF interaction and membrane insertase activity. Biochemistry 45:13401–13408. CrossRefGoogle Scholar
  64. 64.
    Sachelaru I et al (2013) YidC occupies the lateral gate of the SecYEG translocon and is sequentially displaced by a nascent membrane protein. J Biol Chem 288:16295–16307. CrossRefGoogle Scholar
  65. 65.
    Schulze RJ et al (2014) Membrane protein insertion and proton-motive-force-dependent secretion through the bacterial holo-translocon SecYEG-SecDF-YajC-YidC. Proc Natl Acad Sci USA 111:4844–4849. CrossRefGoogle Scholar
  66. 66.
    Chen Y, Soman R, Shanmugam SK, Kuhn A, Dalbey RE (2014) The role of the strictly conserved positively charged residue differs among the Gram-positive, Gram-negative, and chloroplast YidC homologs. J Biol Chem 289:35656–35667. CrossRefGoogle Scholar
  67. 67.
    Shimokawa-Chiba N et al (2015) Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein. Proc Natl Acad Sci USA 112:5063–5068. CrossRefGoogle Scholar
  68. 68.
    Geng Y et al (2015) Role of the cytosolic loop C2 and the C-terminus of YidC in ribosome binding and insertion activity. J Biol Chem 290:17250–17261. CrossRefGoogle Scholar
  69. 69.
    Seitl I, Wickles S, Beckmann R, Kuhn A, Kiefer D (2014) The C-terminal regions of YidC from Rhodopirellula baltica and Oceanicaulis alexandrii bind to ribosomes and partially substitute for SRP receptor function in Escherichia coli. Mol Microbiol 91:408–421. CrossRefGoogle Scholar
  70. 70.
    Chen Y et al (2017) YidC insertase of Escherichia coli: water accessibility and membrane shaping. Structure 25:1403–1414. CrossRefGoogle Scholar
  71. 71.
    Noinaj N et al (2013) Structural insight into the biogenesis of beta-barrel membrane proteins. Nature 501:385–390. CrossRefGoogle Scholar
  72. 72.
    Anghel SA, McGilvray PT, Hegde RS, Keenan RJ (2017) Identification of Oxa1 homologs operating in the eukaryotic endoplasmic reticulum. Cell Rep 21:3708–3716. CrossRefGoogle Scholar
  73. 73.
    Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ (2015) A YidC-like protein in the archaeal plasma membrane. Structure 23:1715–1724. CrossRefGoogle Scholar
  74. 74.
    Nagamori S, Smirnova IN, Kaback HR (2004) Role of YidC in folding of polytopic membrane proteins. J Cell Biol 165:53–62. CrossRefGoogle Scholar
  75. 75.
    Serdiuk T et al (2016) YidC assists the stepwise and stochastic folding of membrane proteins. Nat Chem Biol 12:911–917. CrossRefGoogle Scholar
  76. 76.
    Yu Z, Koningstein G, Pop A, Luirink J (2008) The conserved third transmembrane segment of YidC contacts nascent Escherichia coli inner membrane proteins. J Biol Chem 283:34635–34642. CrossRefGoogle Scholar
  77. 77.
    Botte M et al (2016) A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion. Sci Rep 6:38399. CrossRefGoogle Scholar
  78. 78.
    Urbanus ML et al (2002) Targeting, insertion, and localization of Escherichia coli YidC. J Biol Chem 277:12718–12723CrossRefGoogle Scholar
  79. 79.
    von Heijne G (1986) The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J 5:3021–3027CrossRefGoogle Scholar
  80. 80.
    Itskanov S, Park E (2019) Structure of the posttranslational Sec protein-translocation channel complex from yeast. Science 363:84–87. CrossRefGoogle Scholar
  81. 81.
    Wu X, Cabanos C, Rapoport TA (2019) Structure of the post-translational protein translocation machinery of the ER membrane. Nature 566:136–139. CrossRefGoogle Scholar
  82. 82.
    Sugano Y, Furukawa A, Nureki O, Tanaka Y, Tsukazaki T (2017) SecY-SecA fusion protein retains the ability to mediate protein transport. PLoS ONE 12:e0183434. CrossRefGoogle Scholar
  83. 83.
    Kedrov A, Kusters I, Driessen AJ (2013) Single-molecule studies of bacterial protein translocation. Biochemistry 52:6740–6754. CrossRefGoogle Scholar
  84. 84.
    Taufik I, Kedrov A, Exterkate M, Driessen AJ (2013) Monitoring the activity of single translocons. J Mol Biol 425:4145–4153. CrossRefGoogle Scholar
  85. 85.
    Haruyama T et al (2019) Single unit imaging of membrane protein embedded nanodiscs from two oriented sides by high-speed atomic force microscopy. Structure 27:152–160. CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Nara Institute of Science and TechnologyIkomaJapan

Personalised recommendations