Pigment structure in the FCP-like light-harvesting complex from Chromera velia

•New carotenoid Ifx-l is present in two different binding pockets in CLH.•Violaxanthin is present in only one binding pocket in CLH.•CLH-bound carotenoid molecules are in all-trans configuration.•The analysis of Chl-a keto group frequencies led to an approximated number of 5–7 non-equivalent chlorophyll-binding sites.

Resonance Raman spectroscopy was used to evaluate pigment structure in the FCP-like light-harvesting complex of Chromera velia (Chromera light-harvesting complex or CLH). This antenna protein contains chlorophyll a, violaxanthin and a new isofucoxanthin-like carotenoid (called Ifx-l). We show that Ifx-l is present in two non-equivalent binding pockets with different conformations, having their (0,0) absorption maxima at 515 and 548 nm respectively. In this complex, only one violaxanthin population absorbing at 486 nm is observed. All the CLH-bound carotenoid molecules are in all-trans configuration, and among the two Ifx-l carotenoid molecules, the red one is twisted, as is the red-absorbing lutein in LHCII trimers. Analysis of the carbonyl stretching region for Chl a excitations indicates CLH binds up to seven Chl a molecules in five non-equivalent binding sites, in reasonable agreement with sequence analyses which have identified eight potential coordinating residues. The binding modes and conformations of CLH-bound pigments are discussed with respect to the known structures of LHCII and FCP.

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