Extended Data Table 2 Pigment binding sites of spinach LHCII, CP29 and CP26 in the PSII–LHCII supercomplex

From: Structure of spinach photosystem II–LHCII supercomplex at 3.2 Å resolution

  1. The local resolution of our cryo-EM map has an uneven distribution, as shown in Extended Data Fig. 2b. The core region has a relatively higher resolution (at 3.0–3.5 Å) than in the regions of peripheral antenna system (3.2–4.0 Å), sufficient to identify the number of pigment molecules bound to each antenna complexes and locate their positions. The identities of chlorophylls (Chl a or Chl b) and carotenoids (lutein, neoxanthin or violaxanthin) are assigned mainly by referring to the information obtained from previous work on the high-resolution crystal structures of spinach LHCII12 and CP29 (ref. 14) and the functional architecture of CP26 (ref. 23).
  2. *Central ligands of chlorophylls coordinating the Mg atoms are shown in parentheses.
  3. †As the N-terminal region of CP29 is intact in the cryo-EM structure, its 601 site is occupied by a chlorophyll (tentatively assigned as Chl a) coordinated by Trp14 (corresponding to Tyr24 in LHCII). Owing to proteolysis at the N-terminal region, the chlorophyll at the 601 site in the previous crystal structure of CP29 might have shifted to the nearby 615 site, sharing the same ligand with Chl a611.
  4. ‡Newly identified chlorophyll-binding site in CP29 or CP26.
  5. §The hydrogen bond donors of the C7-formyl group of Chl b molecules are shown in square brackets.
  6. ||These sites in the previous crystal structure of CP29 were occupied by a Chl b (614) and Chl a (615) coordinated by His229 (614) and glycerol-3-phosphate, respectively. They are not observed in the cryo-EM structure reported here. Chl b614 is located at a peripheral site in contact with detergent and might be lost during purification, leading to a vacant site without chlorophyll bound.
  7. ¶These data were extracted and summarized from previous publications14,23,63,64,65,66.