Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c

Abstract

Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 Fe₄S₄ clusters, 12 lipids, 2 Ca²⁺ ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs.

Fig. 1. Two structural forms of the CabRC.

a Structure of the CabRC_S complex viewed along the membrane plane from the front (left) and the periplasmic side (right). b The structure of the CabRC_L complex viewed along the membrane plane from the front (left) and side (right). All subunits are shown as cartoon models of different colors. Carotenoids, lipids and unknown molecules are shown as line models and colored light blue. Only the main tetrapyrrole rings are shown for (B)Chls, and are colored green. Only the main tetrapyrrole rings are shown for heme groups, and are colored hot pink. Fe₄S₄ clusters are shown as yellow and oraspheres.

Fig. 2. Cofactor arrangement of the ETC in the CabRC viewed along the membrane plane and from the periplasmic side.

The center-to-center distances between the cofactors (black dotted lines) are given in Å. The boxed areas show the coordinating environments for all cofactors in the ETC. The cofactors Heme1, Heme2, P₈₄₀, Acc, A₀, and Fe₄S₄ (F_X, F_A, and F_B) are colored orange, salmon red, green, light blue, cyan, and orange/yellow, respectively. The backbone carbon atoms of PME1002 are colored magenta. Calcium ions (Ca²⁺) and water molecules (Wat) are shown as spheres and colored gray and red, respectively. For clarity, the tail of PME1002 is omitted in the boxed areas.

Fig. 3. Comparison of the Ca²⁺-binding environments in homodimeric type I RCs and the Mn₄CaO₅-binding environment in PSII.

a Superposition of the CabRC core with the GsbRC core (PscA homodimer; PDB code: 6M32) and the HbRC core (PshA homodimer; PDB code: 5V8 K) to show the positions of their Ca²⁺-binding sites. b The position of the Mn₄CaO₅ cluster in the PSII RC core (CP43-D1-D2-CP47; PDB code: 3WU2). c Magnified views of the Ca²⁺-binding environments in the CabRC core, GsbRC core, and HbRC core. Calcium ions in the CabRC core, GsbRC core, and HbRC core are colored blue, salmon red, and brown, respectively. d Magnified views of the Mn₄CaO₅-binding environment in PSII. Calcium ions, Mn₄CaO₅, and water molecules are shown as spheres, and the Ca²⁺-coordinating residues are shown as sticks; water molecules, Mn ions, and oxygen atoms are colored yellow, purple, and red, respectively; interactions are indicated by black dotted lines.

Fig. 4. Structures of PscX and PscY and their interactions with the CabRC core.

a The PscX‒PscY subcomplex interacts with the CabRC core at different sites. Details in the square boxes are presented in (b), (e), and (f). b Arrangement of the PscX‒PscY subcomplex in the CabRC. The interface of the two proteins is indicated by a black ellipse. c Superposition of the monoheme binding domains of PscX and PscY. d Hydrogen bonds (black dotted lines) formed between residues at the interface of PscX and PscY. e, f Magnified views of the interactions between PscX or PscY and the CabRC core in the transmembrane region. The brown and green boxes (in left panels) are enlarged, and the enlargements (center) show the main hydrophobic interactions between PscX or PscY and the CabRC core; the hydrophobicity is colored red. The dark blue and cyan boxes are further enlarged, and the enlargements (right) show the hydrogen bonds are indicated by black dotted lines. g Magnified views of the interactions between PscX or PscY and the CabRC core in the periplasmic region. All salt bridges are indicated by red dotted lines.

Fig. 5. Comparison of the F_A-F_B arrangements in membrane-extrinsic electron acceptors.

a Comparison of the primary sequences among three membrane-extrinsic electron acceptors. All conserved residues coordinated to the Fe₄S₄ cluster are indicated with black arrows. This figure was generated using ESPrint 3. b Arrangement of F_X, F_A, and F_B in the CabRC and GsbRC, based on the superposition of their PscB subunits. c Arrangement of F_X, F_A, and F_B in the CabRC and PSI based on the superposition of PscB/CabRC and PsaC/PSI. PDB codes: GsbRC, 6M32; PSI, 1JB0.

Fig. 6. Interactions between PscB and the CabRC core.

a Arrangement of PscB and the CabRC core. The interface is indicated by red ellipse. b Electrostatic potential (calculated with APBS tools) analysis of the binding interface between PscB and the CabRC core. Positive potential is shown in blue (+5 kT/e) and negative potential in red (−5 kT/e). Close-up views of the surfaces of PscB (c) and the CabRC core (d). All residues on the interfaces at a distance of 5 Å or less are shown with sticks.

Fig. 7. Distribution of (B)Chls a and lycopenes and possible ET pathways in the CabRC.

a Pigments in the CabRC are arranged into the cytoplasmic layer (closer to the cytoplasmic side) and periplasmic layer (closer to the periplasmic side). Chls a are colored dark blue, Zn-BChls a′ and BChls a are colored green, and lycopenes are colored brown. Arrangement of pigments at the cytoplasmic layer (b) and periplasmic layer (c), with Mg²⁺-to-Mg²⁺ distances given in Å. d Possible ET pathways in the CabRC. The directions of ET are indicated with red dotted arrows. Chls a and BChls a are represented by dark blue and green spheres, respectively.