Co-crystallization of the human nuclear cap-binding complex with a m⁷GpppG cap analogue using protein engineering

The nuclear cap-binding complex (CBC) binds the 7-methyl-G(5')ppp(5')N cap structure at the 5' end of pre-messenger and uracil-rich small nuclear RNAs in the nucleus. It mediates interaction of these capped RNAs with various nuclear machineries involved in RNA maturation and is co-exported with them to the cytoplasm. The structure of human CBC, which comprises the subunits CBP20 and CBP80, has previously been determined in a mildly trypsinated form which can no longer bind the cap. Here, the engineering and crystallization of two variant CBCs with deletions in CBP80 which do not affect function are described. A complex with a small N-terminal deletion in CBP80 was crystallized in space group C2 with one complex per asymmetric unit. The crystals diffract to 2 Å resolution and give the first structure of intact but cap-free CBC. An additional internal deletion in CBP80 of a prominent solvent-exposed coiled coil gives rise to a more compact complex. This was co-crystallized with the cap analogue m⁷GpppG in two different crystal forms which could grow in the same drop. Form 1 belongs to space group P3₁21 with one complex per asymmetric unit and diffracts to 2.15 Å resolution. Form 2 belongs to space group P2₁2₁2₁ with two complexes per asymmetric unit and diffracts to 2.3 Å resolution. In both forms, strong extra electron density is observed for the cap analogue and for the N- and C-terminal extensions of CBP20 which was absent or disordered in all previous structures.