Extended Data Fig. 1: Starting model and sample snapshots of the β2AR-GsGDP simulations, together with overview of relevant crystal structures. | Nature Structural & Molecular Biology

Extended Data Fig. 1: Starting model and sample snapshots of the β2AR-GsGDP simulations, together with overview of relevant crystal structures.

From: Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor

Extended Data Fig. 1

A1) In the starting model, inactive GsGDP (PDB ID: 6EG8) is placed below the receptor with α5 in an orientation as the 14-mer-peptide derived from the C-terminus of α5, co-crystallized with the β2AR (PDB ID: 6E67)16. Notably, Y391α5 and H387α5, that interact with the receptor in the crystal structure of β2AR-Gsempty (PDB ID: 3SN6, inset A4) are still buried (inset A1), while E392α5 and R389α5, that bind to the receptor in β2AR-GsGDP (inset A2) and in the β2AR-α5-peptide complex6 (inset A3), are solvent exposed and ready to interact. To provide sufficient space for structural adaptations that occur upon complex formation, in the initial model, the side chains of R389α5 and E392α5 were put at 23.5 and 15.0 Å away from the side chains of D1303.49 and R1313.50, respectively. A2) In the β2AR-GsGDP complex, α5 adopts a similar orientation and binding mode as in the β2AR-α5-peptide complex. A3) Crystal structure of the β2AR-α5-peptide complex (PDB ID: 6E67)16, without showing the stabilizing modifications. The minor deviations observed when comparing this complex with the β2AR-GsGDP complex (inset A2), were expected, because of the stabilizing modifications of the β2AR-α5-peptide complex. A4) In β2AR-Gsempty (PDB ID 3SN6) α5 binds differently to the receptor when compared to the previous complexes. The inset shows that Y391α5 and H387α5, that are initially buried in GsGDP (inset A1), engage the receptor in the crystal structure of β2AR-Gsempty, while E392α5 and R389α5, that engage the receptor in the other two complexes, point away from the interface. B) G protein labels for subdomains as typically used in G-protein nomenclature (CGN13). C) Different orientations of α5 (the remainder of the G protein is hidden) relative to the receptor in β2AR-GsGDP when compared to β2AR-Gsempty. Top view of α5 from the cytoplasmic side reveals that α5 is rotated by ca. 40° when the two complexes are compared. The side view highlights the different binding angles of α5 relative to the membrane normal.

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