Table 3.

Intermolecular cross-linked peptides of the activated complex of Gt_α–GDP–AlF₄⁻ with PDE6 holoenzyme

Cross-linked peptides were identified following chemical cross-linking of a mixture of Gt_α–GDP–AlF₄⁻ and PDE6 holoenzyme attached to lipobeads and analyzed as described under “Experimental procedures.” The abbreviations are defined in the legend to Table 1. All identified intra- and intermolecular cross-links involving PDE6 catalytic subunits were identical to those observed in the holoenzyme structure (Table 1 and Ref. 20) and omitted here.

Exp. m/z	z	Δ	pep1	aa1	pep2	aa2	Cross-linker
		ppm
947.4468	2	3.7	Gtα	9	Pα/Pβ	442/440a	EDC
673.5722	4	−4.1	Gtα	10	Pβ	826	BS(PEG)5
447.0946	8	7.8	Gtα	10	Pα	854b	BS3
684.3533	3	−3.1	Gtα	17	Pα	551b	BS3
545.3019	2	2.4	Gtα	17	Pα/Pβ	808/806	EDC
674.0325	3	−1	Gtα	17	Pβ	817	Sulfo-SDA
558.3024	4	−8.9	Gtα	20	Pα/Pβ	807/805	BS3
1360.241	2	4.3	Gtα	20	Pα/Pβ	620/618	BS3
812.4367	3	5.7	Gtα	24	Pα/Pβ	330/328a	Sulfo-SDA
752.024	3	−7.6	Gtα	25	Pα	309c	BS3
775.0531	3	−3.9	Gtα	128	Pα/Pβ	807/805b	BS3
569.994	3	−7.8	Gtα	275	Pβ	307c	BS3
381.2	3	−9.3	Gtα	98	Pγ	41	EDC
332.469	4	1.7	Gtα	275	Pγ	29	BS3
337.8635	3	−7.3	Pα/Pβ	328/326	Pγ	25	EDC
413.2165	5	−14	Pα	551	Pγ	29	BS3

^a Cross-links that were omitted from specific structural models during docking of Gt_α to catalytic domain.

^b Cross-links that were omitted from specific structural models during docking Gt_α to GAFb domain.

^c Cross-links that were omitted from specific structural models from computational modeling due to loop flexibility.