Overall structure of the PSI-FCPI supercomplex from T. pseudonana. Structures are viewed from the stromal side (left panels) and from the direction perpendicular to the membrane normal (right panels). Only protein structures are depicted, with cofactors omitted for clarity. The FCPI (A) and PSI-core (B) subunits are labeled and colored distinctly. The five FCPI subunits are labeled as FCPI-1 to 5 (red), with their corresponding gene products indicated in parentheses (black) in panel A.

Structure and diversity of Psa29. (A) Structure of Psa29 depicted as cartoons. Psa29 was modeled from V47 to L178. (B) Cryo-EM map of Psa29 and its surrounding environment, viewed from the stromal side. The red-squared areas are enlarged in panels C–G. Yellow, PsaB; cyan, PsaC; blue, PsaD; magenta, PsaL; orange, Psa29. (C–G) Protein-protein interactions of Psa29 with PsaB/PsaC (C), PsaC/PsaD (D), PsaB/PsaD (E), PsaB/PsaD/PsaL (F), and PsaD (G). Interactions are indicated by dashed lines, and the numbers are distances in Å. Amino acid residues participating in the interactions are labeled; for example, A71/C indicates Ala71 of PsaC. B, PsaB; C, PsaC; D, PsaD, L, PsaL; 29, Psa29. (H) Phylogenetic analysis of Psa29 in photosynthetic organisms. A maximum-likelihood tree of Psa29 proteins was inferred using IQ-TREE v2.2.2.7 with the WAG+F+G4 model and a trimmed alignment of 22 sequences comprising 245 amino acid residues. Numbers at the nodes represent ultrafast bootstrap support (%) (1000 replicates). The tree was mid-point rooted between diatoms and Bolidophyceae Parmales. Psa29 of T. pseudonana CCMP1335 is indicated by a red underline.

Structural characteristics of FCPI-1 (RedCAP). (A) Interactions of FCPI-1 with PsaB, PsaI, and PsaL viewed from the stromal (left) and lumenal (right) sides. The areas encircled by black squares are enlarged in panels B and C. Yellow, PsaB; magenta, PsaI; dark red, PsaL; red, FCPI-1. (B, C) Protein-protein interactions of FCPI-1 with PsaL (B) and with PsaB/PsaI/PsaL (C). Interactions are indicated by dashed lines, and the numbers are distances in Å. Amino acid residues involved in the interactions are labeled; for example, S139/1 indicates Ser139 of FCPI-1. B, PsaB; I, PsaI; L, PsaL; 1, FCPI-1. (D) Characteristic loop structure from Q96 to T116 in FCPI-1, viewed from the lumenal side. Q96 and T116 are labeled with sticks, and the Q96–T116 loop is colored pink. (E) Superpositions of FCPI-1 with FCPI-2, FCPI-3, FCPI-4, and FCPI-5. Only proteins are depicted. Q96 and T116 in the Q96–T116 loop of FCPI-1 are shown with sticks.

Structural characteristics of FCPI-2. (A) Interactions of FCPI-2 with PsaB and PsaM viewed from the stromal (left) and lumenal (right) sides. The areas encircled by black squares are enlarged in panels B and C. PSI subunits are colored grey, and FCPI subunits are colored yellow. Protein-protein interactions are shown in different colors: green, FCPI-2; cyan, PsaB; pink, PsaM. (B, C) Protein-protein interactions of FCPI-2 with PsaB (B) and PsaM (C). Interactions are indicated by dashed lines, and the numbers represent distances in Å. Amino acid residues involved in the interactions are labeled; for example, Y138/2 indicates Tyr138 of FCPI-2. B, PsaB; M, PsaM; 2, FCPI-2.

Structural characteristics of FCPI-3, 4, and 5. (A) Interactions among FCPIs and between FCPIs and PsaL, viewed from the stromal (left) and lumenal (right) sides. The areas encircled by black squares are enlarged in panels B–D. PSI subunits are colored grey, and FCPI subunits are colored yellow. Protein-protein interactions are shown in different colors: blue, FCPI-3; magenta, FCPI-4; orange, FCPI-5; purple, PsaL. (B–D) Protein-protein interactions between FCPI-3 and PsaL (B), between FCPI-4 and FCPI-5 (C), and between FCPI-5 and PsaL (D). Interactions are indicated by dashed lines, and the numbers represent distances in Å. Amino acid residues involved in the interactions are labeled; for example, L126/3 indicates Leu126 of FCPI-3. L, PsaL; 3, FCPI-3; 4, FCPI-4; 5, FCPI-5.

Comparisons of structures and sequences of FCPIs in the PSI-FCPI structures between T. pseudonana and C. gracilis. (A) Superposition of the PSI-FCPI structures between T. pseudonana and C. gracilis (PDB: 6LY5). FCPI subunits from T. pseudonana and C. gracilis are colored red and cyan, respectively. The structures are viewed from the stromal side. The FCPI-1 to 5 sites are labeled. (B) Correlation of the names of FCPIs in the structures with their corresponding genes between T. pseudonana and C. gracilis. The FCPI genes are derived from Kumazawa et al. (30) and Kato et al. (14) for C. gracilis. (C) Phylogenetic analysis of FCPs and RedCAPs from T. pseudonana (Tp) and C. gracilis (Cg). In addition to the RedCAP family, 44 TpFCPs and 46 CgFCPs are grouped into five Lhc subfamilies and CgLhcr9 homologs. Maroon, RedCAP family; magenta, Lhcq subfamily; red, Lhcz subfamily; orange, Lhcr subfamily; brown, CgLhcr9 homologs; green, Lhcf subfamily; blue, Lhcx subfamily. The FCPs and RedCAPs located at the FCPI-1 to 5 sites are labeled. The tree was inferred using IQ-TREE 2 (59) with the Q.pfam + R4 model selected by ModelFinder (60). The light purple circular symbols on the tree represent bootstrap support (%).