Photosynthesis relies on energy transfer from light-harvesting complexes to reaction centers. Phycobilisomes, the light-harvesting antennas in cyanobacteria and red algae, attach to the membrane via the multidomain core-membrane linker, L CM . The chromophore domain of L CM forms a bottleneck for funneling the harvested energy either productively to reaction centers or, in case of light overload, to quenchers like orange carotenoid protein (OCP) that prevent photodamage. The crystal structure of the solubly modified chromophore domain from Nostoc sp. PCC7120 was resolved at 2.2 Å. Although its protein fold is similar to the protein folds of phycobiliproteins, the phycocyanobilin (PCB) chromophore adopts ZZZssa geometry, which is unknown among phycobiliproteins but characteristic for sensory photoreceptors (phytochromes and cyanobacteriochromes). However, chromophore photoisomerization is inhibited in L CM by tight packing. The ZZZssa geometry of the chromophore and π-π stacking with a neighboring Trp account for the functionally relevant extreme spectral red shift of L CM . Exciton coupling is excluded by the large distance between two PCBs in a homodimer and by preservation of the spectral features in monomers. The structure also indicates a distinct flexibility that could be involved in quenching. The conclusions from the crystal structure are supported by femtosecond transient absorption spectra in solution.cyanobacteria | phycobilisome | core-membrane linker | photosynthesis | crystal structure T he structural separation of light-harvesting and energy transduction processes allows photosynthetic organisms a flexible adaptation to the diverse light regimes present in terrestrial and aqueous habitats. In cyanobacteria and some phylogenetically related organisms that, together, provide a substantial proportion of global carbon fixation, light is harvested by hundreds of chromophores located in the peripheral antenna, namely, the phycobilisome (PBS). These excitations are then collected and transferred to the energy-transducing photosystems I (PSI) and PSII in the photosynthetic membrane via only two pigments, allophycocyanin B (AP-B) and the core-membrane linker (L CM ) (1-5). AP-B preferentially serves PSI (2); it is structurally similar to the bulk phycobiliproteins of the PBS (6). L CM (denoted as ApcE according to the gene by which it is encoded), preferentially serving PSII (5), is a more complex multidomain protein, with an N-terminal section that binds the phycocyanobilin (PCB) chromophore, and is homologous to phycobiliproteins but carries an additional loop that probably acts as a membrane anchor to PSII (4, 7-10). The Cterminal section consists of two to four repeats (depending on the PBS type) that are homologous to the N-terminal domain (Pfam PF00427) of structural PBS proteins, rod-linkers [Protein Data Bank (PDB) ID codes 3OSJ and 3OHW], and considered to organize the complex PBS core (9). They are probably also the loci for phosphorylation (11).Both AP-B and L CM contain the same PCB chromophores...