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Crystal structure of a substrate-engaged SecY protein-translocation channel

Abstract

Hydrophobic signal sequences target secretory polypeptides to a protein-conducting channel formed by a heterotrimeric membrane protein complex, the prokaryotic SecY or eukaryotic Sec61 complex. How signal sequences are recognized is poorly understood, particularly because they are diverse in sequence and length. Structures of the inactive channel show that the largest subunit, SecY or Sec61α, consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces lipid1,2,3,4,5,6,7,8,9,10. The cytoplasmic funnel is empty, while the extracellular funnel is filled with a plug domain. In bacteria, the SecY channel associates with the translating ribosome in co-translational translocation, and with the SecA ATPase in post-translational translocation11. How a translocating polypeptide inserts into the channel is uncertain, as cryo-electron microscopy structures of the active channel have a relatively low resolution (~10 Å) or are of insufficient quality6,7,8. Here we report a crystal structure of the active channel, assembled from SecY complex, the SecA ATPase, and a segment of a secretory protein fused into SecA. The translocating protein segment inserts into the channel as a loop, displacing the plug domain. The hydrophobic core of the signal sequence forms a helix that sits in a groove outside the lateral gate, while the following polypeptide segment intercalates into the gate. The carboxy (C)-terminal section of the polypeptide loop is located in the channel, surrounded by residues of the pore ring. Thus, during translocation, the hydrophobic segments of signal sequences, and probably bilayer-spanning domains of nascent membrane proteins, exit the lateral gate and dock at a specific site that faces the lipid phase.

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Figure 1: Architecture of the active SecY channel.
Figure 2: Conformational changes of the SecY channel.
Figure 3: The polypeptide in the channel.
Figure 4: Scheme of SecA-mediated protein translocation.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The crystal structure determined in this study has been deposited in the Protein Data Bank (PDB) under accession number 5EUL.

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Acknowledgements

We thank C. Martone and for help with nanobody generation and cloning, C. Shoemaker and J. Mukherjee for their assistance in alpaca immunization, A. Whynot for cloning G. thermodenitrificans SecY, and H. Suzuki and T. Walz for help with fluorescence size-exclusion chromatography. We thank the staff at Northeastern Collaborative Access Team (NE-CAT) of the Advanced Photon Source, the SBGrid consortium at Harvard Medical School, the organizers of the CCP4/Advanced Photon Source summer school 2015, and the beam host at GMCA-CAT. We thank A. Salic and T. Guettler for reading the manuscript. The work was supported by National Institutes of Health grants to T.A.R. (GM052586) and by a Pioneer Award to H.P. T.A.R. is a Howard Hughes Medical Institute investigator.

Author information

Authors and Affiliations

Authors

Contributions

E.P. designed the SecA–substrate fusion constructs, performed biochemical tests, and obtained the initial crystals; L.L. optimized constructs and crystals, performed biochemical tests, screened nanobodies, and determined the crystal structures; J.L., J.I., and H.P. generated and cloned nanobodies; T.A.R., L.L., and E.P. interpreted the structure and wrote the manuscript. T.A.R. supervised the project.

Corresponding authors

Correspondence to Long Li or Tom A. Rapoport.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Generation of translocation intermediates with a three-component system.

a, Strategy to generate SecA-dependent translocation intermediates in E. coli cells. The intermediates are assembled from E. coli SecA, E. coli SecY complex, and substrate containing an N-terminal OmpA signal sequence and C-terminal superfolder GFP51 (sfGFP). After loop insertion into the SecY channel, translocation of the C terminus is stalled by the folded sfGFP. Insertion is monitored by disulfide bond formation between a pair of cysteines introduced into the substrate and the plug of SecY (yellow stars). b, Scheme showing the simplified system, in which a secretory protein segment is fused into the two-helix finger of SecA. c, Sequence of the substrate used in a. The −1 position of the original signal sequence was changed to Tyr to prevent signal sequence cleavage. The position of the cysteine and the length of the translocated segment were varied (here shown for Cys at position +3 and 58 amino acids in length). d, Variation of the Cys position with a translocationg segment of 58 residues. Where indicated, disulfide crosslinks to SecY with a Cys at position 68 (OmpA–GFPxSecY) were induced by the oxidant copper phenanthroline (CuPh) before harvesting the cells. The samples were analysed by non-reducing SDS–PAGE, followed by western blotting (WB) with anti-SecY and anti-GFP antibodies. e, As in d, but in the absence of oxidant, with Cys at different positions and variation of the length of the translocated segment. Asterisks indicate non-specific bands. f, As in e, but with E. coli cells expressing B. subtilis (B.s.) SecA and G. thermodenitrificans (G.t.) SecYE. The substrate contained a Cys at position +7, and SecY a Cys at position 60. The red arrows indicate spontaneously generated disulfide crosslinks (GFP sometimes does not unfold in SDS, resulting in two bands). The OmpA–GFP constructs contained a C-terminal Strep-tag that was detected by StrepTactin conjugated with horseradish peroxidase (HRP).

Extended Data Figure 2 Generation of translocation complexes with SecA–substrate fusion constructs.

a, Translocation complexes were generated as indicated in the scheme in Extended Data Fig. 1b. An E. coli SecA–substrate fusion (SecA-OAIns74 (L12)) was overexpressed together with E. coli SecY complex in E. coli cells. SecA-OAIns74 (L12) contains 74 amino acids inserted into the two-helix finger of SecA, including a linker of 12 residues, and a GFP tag following SecA. Translocation of the substrate segment was monitored by spontaneous disulfide crosslinking between a cysteine at position +7 (with respect to the original signal peptidase cleavage site) and a cysteine at position 68 in the plug of SecY. Where indicated, β-mercaptoethanol (β-ME) was added to reduce the disulfide bond. The samples were analysed by non-reducing SDS–PAGE and western blotting with anti-SecY antibodies. The overexpression of SecA-OAIns was monitored by the fluorescence of GFP (data not shown) and staining with Coomassie blue (CBB, lower panel). b, As in a, but with E. coli SecA-OAIns constructs containing from 6 to 12 residues in the linker (L6–L12) or mutations (3Q) in the H-region of the signal sequence. Expression of SecA-OAIns was verified by the strong green fluorescence of cell lysates, caused by GFP fused to the C terminus of SecA (not shown). The lower panel shows the sequences of the SecA-inserted segments. c, As in a, but with B. subtilis SecA-OAIns74 (L12) and G. thermodenitrificans SecYE. SecY and SecA were detected by western blotting with anti-His antibodies and Ponceau staining, respectively. d, As in c, but with B. subtilis SecA-OAIns containing different inserted segments. SecA-OAIns was expressed under different conditions, as indicated. Expression of SecA-OAIns was verified by green fluorescence of GFP fused to the C terminus of SecA (not shown) and Ponceau staining (second panel). The sequences of the constructs are shown in the lowest panel. e, As in d, but with different constructs, the sequences of which are shown in the lower panel. Where indicated, copper phenanthroline (CuPh) was added to the cells to induce disulfide bridge formation. SecA-OAIns49(L7) was used for crystallization. f, As in e, but with a Cys at position −1 (the last residue of the OmpA signal sequence) instead of position +7. Note that in this case disulfide formation does not occur spontaneously.

Extended Data Figure 3 Purification of an active translocation complex.

a, Scheme of the purification protocol. b, Elution of the G. thermodenitrificans SecYE/B. subtilis SecA-OAIns complex from a Superdex200 column during the last chromatography step. c, Non-reducing SDS–PAGE analysis of samples taken during the purification procedure and of fractions indicated with red numbers in b. Lane 1, molecular mass markers. Lane 2, sample analysed after immobilized metal ion affinity chromatography. Lane 3, sample after cleavage of the GFP tag. Lane 4, sample after anion exchange chromatography (MonoQ).

Extended Data Figure 4 Electron density map and refined model.

a, Stereo view of the unsharpened density map (2Fo – Fc; 1σ) of the entire complex. Heavy metal ion clusters are shown in yellow. b, As in a, but with the density map derived from MAD phasing after density modification. c, SigmaA-weighted phase-combined 2Fo – Fc density maps of the translocating peptide region. Left: omit map calculated without a model for the translocating peptide. Right: map calculated with the model. Phe (−7) is one of the residues used to determine the registry of the helix. d, A side view of the density for TM3 and TM4. e, Density showing the disulfide crosslink between the plug and translocating chain. f, Top view of Gly19 of the translocating chain surrounded by pore residues.

Extended Data Figure 5 Interactions of the nanobody and SecA with SecY.

a, The nanobody binds to the plug and to the loop between TM3 and TM4 (L3/4). b, The polypeptide crosslinking domain (PPXD; in yellow) of SecA interacts with the loop between TM8 and TM9 of SecY (L8/9; in red), and the long helix of the helical scaffold domain (HSD; in blue) with the loop between TM2 and TM3 (L2/3; in red). The loop between TM6 and TM7 of SecY (L6/7; in red) does not seem to make strong contact with SecA. c, Two helices of the HSD interact with the C-terminal tail of SecY (C-tail; in red).

Extended Data Figure 6 Comparison of the conformations of SecA in the active G. thermodenitrificans and inactive T. maritima complexes.

The domains of SecA in the G. thermodenitrificans complex are labelled with different colours (nucleotide binding domain 1 (NBD1), blue; nucleotide binding domain 2 (NBD2), cyan; helical scaffold domain (HSD), brown; helical wing domain (HWD), grey; polypeptide crosslinking domain (PPXD), yellow). SecA in the T. maritima complex is shown in pink. Left: a top view (the channel would be underneath); right: a side view with the two-helix finger (part of helical scaffold domain) indicated.

Extended Data Figure 7 Localization of signal sequences in the G. thermodenitrificans SecY and mammalian Sec61 channels and of a TM domain in the mammalian Sec61 channel.

a, In the active channel (salmon), the signal sequence displaces TM7 and TM8 in the idle T. thermophilus channel (cyan). b, As in a, but comparison with the idle M. jannaschii channel (tan). The C-region of the signal sequence takes the position of TM7. c, Side view of the interactions of the H-region of the signal sequence with TM2 of G. thermodenitrificans SecY. Interacting amino acids are indicated. d, Stereo view showing the intercalation of the C-region into the periplasmic side of the lateral gate. Residues of the amphipathic helix are indicated. e, The active G. thermodenitrificans channel (in salmon) was aligned with a mammalian channel (in grey) containing a nascent membrane protein (PDB accession number 4CG6) using secondary structure matching47. The signal sequence in the bacterial channel is shown in green, and the TM segment of the nascent membrane protein in yellow. f, As in e, but comparison of the active G. thermodenitrificans channel with a mammalian Sec61 channel (light blue) containing a secretory protein fragment (PDB accession number 3JC2). The signal sequences are shown in green and yellow, respectively.

Extended Data Figure 8 The plug domains in SecY channels.

a, The plugs in channels of different organisms have different structures. Shown are side views with the plugs in yellow and pore residues as red spheres. PDB accession numbers are given below the names of the organisms. For the G. thermodenitrificans channel, the translocating peptide segment was omitted. b, In the inactive T. maritima SecY channel, the plug (in yellow) is at the front of the channel, partly sealing the periplasmic side of the lateral gate. Shown is a side view in a surface representation, with hydrophilic and hydrophobic residues in blue and orange, respectively.

Extended Data Figure 9 Structures of the active G. thermodenitrificans complex determined without nanobody or with a different signal sequence.

a, Stereo view of density maps at 6.5 Å resolution for the active complex in the absence of nanobody. Shown is a 2Fo – Fc density map at 1σ (blue mesh) and a difference map (Fo – Fc) at 3σ (green mesh), both calculated by molecular replacement with a model lacking the plug. Strong positive density is seen close to SecE, probably corresponding to parts of the plug. The arrow indicates the movement of the plug from the position in the structure with nanobody to the density seen in the structure without nanobody. b, Stereo views of density maps at ~8.5 Å resolution for the active G. thermodenitrificans complex in which the OmpA signal sequence was replaced by that of DsbA. Shown is a side view of the 2Fo – Fc density map at 1σ (blue mesh) and a difference map (Fo – Fc) at 3σ (green mesh), both calculated by molecular replacement with a model lacking the signal sequence. Note that the model for the OmpA signal sequence fits well into the density corresponding to the DsbA signal sequence. c, As in b, but top view and not in stereo.

Extended Data Table 1 Data collection and refinement statistics for MAD structures

Supplementary information

Supplementary Figure 1

This file contains the uncropped scans, with size marker indication, for Extended Data Figures 1, 2 and 3. (PDF 926 kb)

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Li, L., Park, E., Ling, J. et al. Crystal structure of a substrate-engaged SecY protein-translocation channel. Nature 531, 395–399 (2016). https://doi.org/10.1038/nature17163

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