a, Stereo image of the cryo-EM density of CP29 bound in the PSII–LHCII supercomplex. b, Superposition of cryo-EM structure of full-length CP29 with the previous crystal structure. Note: Chls a601 and a616 are newly observed in the cryo-EM structure of CP29. Chl a601 might account for the electron density of Chl a615 observed in the crystal structure of spinach CP29 (ref. 14). Compared to Chl a601, a615 is much closer to a611 owing to the loss of the N-terminal domain caused by proteolysis. Chl b614 is a peripheral chlorophyll found in the crystal structure, but is probably lost during purification and therefore not observed in the cryo-EM structure. Orange, cryo-EM structure; cyan, crystal structure. c, Superposition of CP29 (orange) with the structure of an LHCII monomer (green). For the cofactors, only Chl a601 is shown; the others are omitted for clarity. d, Cryo-EM density of Chl a601 in CP29. e, Cryo-EM density of Chl a616 at the interface between CP29 and CP47. f, Superposition of Lhca3 and Lhca4 structures with that of CP29 in the PSII–LHCII supercomplex. Chl a616 (CP29) and a617 (Lhca3/4) molecules are shown as stick models; the other cofactors are omitted for clarity. Orange, CP29; magenta, Lhca3; blue, Lhca4. PDB codes: 4XK8, Lhca3 and Lhca4 from the PSI–LHCI supercomplex; 1RWT, LHCII.