Sec61 Translocon: Structure, Transport, and Inhibition

Proteins destined for secretion or membrane integration rely on the Sec61 translocon, a crucial channel in the endoplasmic reticulum (ER). This protein complex ensures proper transport and folding, playing an essential role in cellular homeostasis.

Structural Features

The Sec61 translocon is a heterotrimeric protein complex embedded in the ER membrane, forming a dynamic channel for nascent polypeptides. It consists of three core subunits: Sec61α, Sec61β, and Sec61γ. The largest and most functionally significant, Sec61α, forms the central pore through which proteins pass. Cryo-electron microscopy and X-ray crystallography reveal that Sec61α adopts a “clam-shell” conformation, with a lateral gate allowing transmembrane domain integration.

A constriction ring of hydrophobic residues prevents ion leakage when the channel is inactive, while a plug domain within Sec61α seals the pore. When a ribosome docks onto the translocon, the plug displaces, aligning the ribosomal exit tunnel with the translocon pore to create a continuous conduit for protein synthesis and translocation.

Sec61 interacts with accessory proteins that modulate its function. The translocon-associated protein (TRAP) complex enhances translocation efficiency, while the oligosaccharyltransferase (OST) complex facilitates co-translational glycosylation. The Sec62/Sec63 complex assists in post-translational translocation, particularly for proteins that do not require ribosome-driven insertion. These auxiliary factors expand Sec61’s functional versatility, accommodating a diverse range of substrates.

Protein Transport Process

Sec61 orchestrates both co-translational and post-translational transport. In the predominant co-translational pathway, the signal recognition particle (SRP) detects an emerging N-terminal signal sequence and directs the ribosome-polypeptide complex to the ER membrane. The SRP receptor facilitates ribosome transfer to Sec61, triggering conformational changes that displace the plug domain and align the ribosomal exit tunnel with the Sec61 pore. This creates a seamless channel for the growing polypeptide to enter the ER lumen.

As elongation progresses, the translocon accommodates the nascent chain, ensuring efficient passage while preventing premature folding. Hydrophobic segments are recognized by the lateral gate, allowing membrane proteins to integrate into the lipid bilayer. This process maintains the correct orientation of transmembrane domains, with positively charged residues favoring cytosolic retention. For soluble proteins, molecular chaperones like BiP bind exposed hydrophobic regions to prevent aggregation and facilitate proper folding.

Certain proteins rely on post-translational transport, particularly those lacking strong ribosome-binding sequences. In these cases, Sec61 operates with the Sec62/Sec63 complex, which recruits BiP to drive polypeptide movement using an ATP-dependent ratcheting mechanism. This pathway is essential for proteins requiring extensive chaperone assistance before reaching their final conformation, highlighting Sec61’s adaptability.

Interplay With ER Quality Control

Sec61 plays a key role in ER quality control, ensuring only properly folded proteins proceed through the secretory pathway. As nascent polypeptides emerge, they encounter chaperones and folding enzymes that assess their structural integrity. Misfolded proteins are retained in the ER, preventing cellular disruption.

Proteins that cannot be rescued by refolding are targeted for degradation through ER-associated degradation (ERAD). In this process, aberrant proteins are extracted from the ER and retrotranslocated through Sec61 into the cytosol, where they are ubiquitinated and degraded by the proteasome. This bidirectional function is regulated by accessory proteins such as Derlin-1 and Hrd1, which help identify misfolded substrates and recruit them to Sec61 for export.

Inhibition Mechanisms

Targeting Sec61 for inhibition has become an area of interest in both research and therapeutic development. Small molecules like cotransin and apratoxin A interfere with distinct stages of the translocation process. Cotransin selectively blocks the translocation of specific substrates, while apratoxin A prevents co-translational translocation altogether, depleting secretory and membrane proteins.

Structural studies reveal how inhibitors engage Sec61 to disrupt its activity. Cryo-electron microscopy shows apratoxin A stabilizing a closed Sec61 conformation, preventing ribosome docking and polypeptide passage. Cotransin appears to interfere with lateral gate dynamics, selectively hindering certain substrates from integrating into the membrane. This mechanistic diversity suggests Sec61 inhibitors could be tailored for therapeutic applications.

Links to Cellular Disorders

Disruptions in Sec61 function are linked to disorders involving protein misfolding and trafficking defects. Mutations or dysregulation of Sec61 can cause misprocessed protein accumulation, triggering ER stress and maladaptive responses. This is evident in congenital disorders like Sec61-related autosomal dominant tubulointerstitial kidney disease (ADTKD-Sec61A1), where defective protein transport in renal epithelial cells leads to progressive kidney failure. Similar mutations are associated with immune deficiencies, where impaired translocation of antigen-presenting proteins compromises cellular defense mechanisms.

Sec61 dysfunction is also implicated in neurodegenerative diseases characterized by protein aggregation. In conditions such as amyotrophic lateral sclerosis (ALS) and Alzheimer’s disease, disruptions in ER protein homeostasis contribute to neuronal toxicity. Studies show Sec61 inhibition exacerbates ER stress, increasing misfolded protein burden and apoptosis. However, pharmacological modulation of Sec61 is being explored to limit the secretion of pathogenic proteins in diseases like multiple myeloma, where malignant cells rely on heightened secretory activity for survival. Sec61’s role in protein quality control underscores its broader relevance in cellular pathology, making it a potential therapeutic target.