Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium Chlorobaculum tepidum

Abstract

Light energy absorption and transfer are very important processes in photosynthesis. In green sulfur bacteria light is absorbed primarily by the chlorosomes and its energy is transferred via the Fenna-Matthews-Olson (FMO) proteins to a homodimeric reaction center (RC). Here, we report the cryogenic electron microscopic structure of the intact FMO-RC apparatus from Chlorobaculum tepidum at 2.5 Å resolution. The FMO-RC apparatus presents an asymmetric architecture and contains two FMO trimers that show different interaction patterns with the RC core. Furthermore, the two permanently bound transmembrane subunits PscC, which donate electrons to the special pair, interact only with the two large PscA subunits. This structure fills an important gap in our understanding of the transfer of energy from antenna to the electron transport chain of this RC and the transfer of electrons from reduced sulfur compounds to the special pair.

Keywords: Chlorobaculum tepidum; Cryo-EM; green sulfur bacterium; photosynthesis; reaction center.

Fig. 1.

Cryo-EM structure of whole FMO-GsbRC complex. (A and C) Overall structure of the whole FMO-GsbRC complex from C. tepidum with views from the side (A) and top (C). Individual subunits are shown in cartoon representation and colored differently. Cofactors (chlorophylls, lipids, carotenoids and Fe-S clusters) are shown as ball-and-stick structures in wheat. (B) Surface representation of the cryo-EM density map (2.5 Å) of the whole FMO-GsbRC colored as in A. (D) Arrangement of the TMHs and the pigments of the whole FMO-GsbRC. TMHs of the two PscA subunits are colored in blue and labeled 1 to 11, from N- to C-terminus. TMHs of the two PscC subunits are colored in yellow and labeled 1 to 3, from N- to C-terminus. Chlorophylls are shown as sticks in grey, with the magnesium ions in pink.

Fig. 2.

Schematic representation of the intersubunit interactions. (A) The intrinsic interactions between subunits of the FMO-GsbRC complex shown as dotted lines. Node sizes are proportional to the solvent accessible surface area of each subunit. Buried surface areas between subunits are listed in SI Appendix, Table S2. (B1) Interaction between PscC (yellow) and PscA (blue). (B2) Interaction of the three TMHs of PscC with the PscA and the energy and electron transport chromophores. (B3) Interaction of the periplasmic loop of PscC with PscA. (C1) Interaction between PscB (orange) and the first FMO trimer (green). (C2) Interaction between the N-arm of PscB and FMO-2. (C3) Interaction between the C-arm of PscB and FMO-1. Interacting residues from PscB, which form salt bridges with various residues of FMO, are labeled. The electrostatic surface potential of FMO proteins is shown from −10 kT/e (red) to +10 kT/e (blue). (D1) Interaction between PscD (pink), the second FMO trimer (purple) and PscA-2 (blue). (D2) Interaction between the second FMO trimer and PscA-2. (D3) Interaction between the second FMO trimer and PscD. All interfacing residues are colored. Residues forming salt bridges are labeled.

Fig. 3.

Asymmetrical arrangement of the two FMO trimers. (A) The two PscA subunits are related by a twofold symmetry axis (C₂, blue line) perpendicular to the membrane plane. The threefold symmetry (C₃) axes of the first and second FMO trimer are indicated as green and purple lines, respectively. From this side view, the C3 axes of the first and second FMO trimer form a 3.5° and 3.0° angle with the membrane normal. (B) Similar to A but rotated ± 90° around the membrane normal. Two side views are related by a 180° rotation. (C) Comparison of both FMO trimers. The first FMO trimer is horizontally moved to align with the second FMO trimer. The two C3 axes are related by a 5.6° rotation. The membrane boundary was defined by the PPM server (31).

Fig. 4.

Possible energy transfer pathways in the FMO-GsbRC complex. (A) Putative energy transfer pathways from chlorosome via the FMO trimers and eventually to GsbRC. Areas in the dashed boxes are enlarged in subsequent panels. (B) Intermolecular interface between the first FMO trimer and PscA-1. (C) Intermolecular interface between the second FMO trimer and PscA-2. (D) Cofactor arrangement along the electron transport chain in GsbRC. The left panel shows the coordinating environment for the three chlorophyll cofactors. The coordinating residues are indicated, and the water molecule serving as an axial ligand to A₀ is shown as a red sphere. (E) Possible energy transfer from BChls to the special pair P₈₄₀. Antenna BChls (811, 814 and 815) are located between the bulk BChls of RC and electron transport chain in the periplasmic BChl layer. All Chl molecules are colored according to the scheme used in Fig. 1. ET cofactors are colored differently for better viewing: P₈₄₀ (orange), A_CC (green), and A₀ (purple). The phytyl tails of BChls and Chls were truncated for ease of viewing. Center-to-center or edge-to-edge distances are indicated as dashed lines and in angstrom (red numbers).

Fig. 5.

Possible electron transport in the FMO-GsbRC complex. (A) Electrostatic surface representation of the FMO-GsbRC complex showing the potential docking site for cyt. c_z. The Left panel shows the periplasmic side of PscA without cyt. c_z, the Middle panel shows the cyt. c_z alone and the Right panel shows the complex with the binding of cyt. c_z. The PscC subunits are shown in cartoon representation. The protein surface is colored according to its electrostatic potential from red (−10 kT) to blue (+10 kT). Residues, which may be involved in a specific binding of cyt. c_z, are indicated. (B) Enlarged views of the potential cyt. c_z docking site. The binding site enclosed by the dashed box is enlarged in the Right panel. The distances of the heme iron to the Mg²⁺ ions of P₈₄₀ are 23.3 and 21.9 Å (red dotted lines), respectively. The propionate group of ring C is at a distance of 2.4 Å from W601^PscA. (C) Electrostatic surface representation of the FMO-GsbRC complex showing the potential docking site for ferredoxin. A homology model of the ferredoxin from C. tepidum (Uniprot: Q8KCZ6) was built using Alphafold. Several positively charged residues are in the proximity of the potential docking site (enlarged view in the Right).