Research Article

A structure of human Scap bound to Insig-2 suggests how their interaction is regulated by sterols

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Science  05 Mar 2021:
Vol. 371, Issue 6533, eabb2224
DOI: 10.1126/science.abb2224

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A cellular cholesterol sensor

Cholesterol levels in cells are controlled by the sterol regulatory element–binding protein (SREBP) pathway. When the cell has sufficient cholesterol, the transcription factor that regulates cholesterol metabolism is sequestered at the endoplasmic reticulum membrane, but when cholesterol is depleted, the transcription factor is released to activate the expression of genes involved in cholesterol synthesis and uptake. Yan et al. determined the structure of a central complex in human SREBP containing the proteins Scap and Insig-2. These two membrane-embedded proteins undergo 25-hydroxycholesterol (25HC)–dependent association and must dissociate for the pathway to be activated. The structure shows that 25HC is sandwiched between Scap and Insig-2 to facilitate their association. A mutational analysis is consistent with the structural model.

Science, this issue p. eabb2224

Structured Abstract

INTRODUCTION

Cholesterol homeostasis is controlled by the sterol regulatory element–binding protein (SREBP) pathway. SREBPs (SREBP-1a, -1c, and -2) are transcription factors with an N-terminal transcription factor domain and a C-terminal regulatory domain (CTD) connected by a transmembrane (TM) hairpin. Among the key players in this pathway, two membrane proteins—Scap and Insig (Insig-1 or -2)—together monitor the sterol level in the endoplasmic reticulum (ER) membrane.

SREBP-CTD constitutively interacts with the C-terminal WD40 domain of Scap. The N terminus of Scap comprises eight TM segments, among which S2 to S6 constitute the sterol-sensing domain (SSD). The SSD is also found in several membrane proteins that are involved in cholesterol metabolism or transport. When the cellular cholesterol level surpasses a certain threshold, the SREBP-2–Scap complex is anchored to the ER membrane through a sterol-dependent interaction between the Scap-SSD and Insig. The interaction is more sensitive to some cholesterol derivatives, like 25-hydroxycholesterol (25HC), than to cholesterol. When cholesterol levels drop, Scap dissociates from Insig. The SREBP-2–Scap complex is subsequently translocated by the COPII vesicles to the Golgi, where the transcription factor domain of SREBP-2 is liberated after two sequential proteolytic cleavages and is transported into the nucleus to activate gene expression for cholesterol synthesis and uptake. Despite rigorous characterizations, the molecular basis for sterol-regulated interaction between Scap and Insig remains elusive.

RATIONALE

The structure of the Scap-Insig-25HC ternary complex will not only reveal the basis for sterol sensing by Scap and Insig but also facilitate the development of potential therapeutics against viral infections and for cancer treatment. Modern methods of single-particle cryo–electron microscopy (cryo-EM) provide a powerful tool to elucidate the structure of this relatively small and highly dynamic membrane protein complex.

RESULTS

WD40-deleted human Scap (residues 1 to 752) and full-length human Insig-2 were transiently coexpressed in HEK293F cells. Supplementation of 25HC during protein expression and isolation was necessary to maintain an intact complex. For cryo-EM analysis, a guided multireference three-dimensional classification method was combined with Relion and CryoSparc. The TM region was determined at resolutions of 3.3 to 3.9 Å, whereas the luminal domains were of lower resolutions, insufficient for model building. Seven TMs—including the entire SSD—in Scap and all six TMs in Insig-2 were resolved.

TMs 1, 2, 3, and 6 of Insig-2 enclose a hydrophobic pocket in which there is no density corresponding to a sterol. A stretch of density that can perfectly fit 25HC is sandwiched by the two proteins in the luminal leaflet of the membrane. Whereas the binding site is mainly constituted by hydrophobic residues on TMs 3 and 4 of Insig-2 and S4, S5, and S6 of Scap, the 25-OH group at the end of the iso-octanol tail of 25HC is exposed to the cytosolic milieu through a hydrophilic cavity enclosed by Scap and Insig-2, which affords a potential explanation for the preference of 25HC over cholesterol in promoting the interaction between Scap and Insig.

S4 in Scap is broken in the middle, resulting in two half helices, S4a and S4b. Compared with the structures of SSD-containing proteins NPC1 and patched 1, in which S4 is straight, the tilting of S4a toward the interior of the SSD creates the space for 25HC accommodation and for the displacement of S2, which constitutes a major interface with Insig. The sandwiched 25HC functions as more than a molecular glue. Its presence stabilizes the unwound conformation of Scap-S4 that is crucial for Insig association. Scap mutations, such as D428A (Asp428 → Ala) and Q432A (Gln432 → Ala), that may lower the energy penalty for S4 unwinding, allow for complex formation with Insig in the absence of sterols. Therefore, the interdependence of S4 unwinding, 25HC accommodation, and Insig binding establishes the molecular basis for sterol sensing.

CONCLUSION

The cryo-EM structure of the human Scap and Insig-2 complex bound to 25HC, together with biochemical analyses, shed light on the mechanistic understanding of sterol sensing in the SREBP pathway. Unwinding of Scap-S4 serves as the switch for 25HC binding and Insig association. Our studies also provide structural interpretations for two well-characterized Scap mutations, the gain-of-function D428A and loss-of-function Y298C (Tyr298 → Cys).

Cryo-EM structure of the complex of human Scap and Insig-2 in the presence of 25HC.

(Left) The TM region of the complex was resolved at resolutions of 3.3 to 3.9 Å, with the highest resolution at the interface between the two proteins. Insig-2 is colored cyan, the SSD of Scap is colored yellow, and the last four resolved residues 447MELA450 of Scap are colored orange. A 25HC molecule is sandwiched between Scap and Insig-2 in the luminal leaflet of the membrane. Formation of the 25HC binding pocket in the complex requires the unwinding of the S4 segment of Scap in the middle of the membrane. The density for 25HC, shown as the blue mesh, is contoured at 5 σ. TH1, transverse helix 1. (Right) A cartoon of the complex structure highlights the 25HC binding site, the broken Scap-S4, and a hydrophobic central pocket in Insig-2. MELADL, the Scap motif that can be recognized by COPII.

Abstract

The sterol regulatory element–binding protein (SREBP) pathway controls cellular homeostasis of sterols. The key players in this pathway, Scap and Insig-1 and -2, are membrane-embedded sterol sensors. The 25-hydroxycholesterol (25HC)–dependent association of Scap and Insig acts as the master switch for the SREBP pathway. Here, we present cryo–electron microscopy analysis of the human Scap and Insig-2 complex in the presence of 25HC, with the transmembrane (TM) domains determined at an average resolution of 3.7 angstrom. The sterol-sensing domain in Scap and all six TMs in Insig-2 were resolved. A 25HC molecule is sandwiched between the S4 to S6 segments in Scap and TMs 3 and 4 in Insig-2 in the luminal leaflet of the membrane. Unwinding of the middle of the Scap-S4 segment is crucial for 25HC binding and Insig association.

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