Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex at 2.5 Å

Abstract

The reaction centre light-harvesting 1 (RC-LH1) complex is the core functional component of bacterial photosynthesis. We determined the cryo-electron microscopy (cryo-EM) structure of the RC-LH1 complex from Rhodospirillum rubrum at 2.5 Å resolution, which reveals a unique monomeric bacteriochlorophyll with a phospholipid ligand in the gap between the RC and LH1 complexes. The LH1 complex comprises a circular array of 16 αβ-polypeptide subunits that completely surrounds the RC, with a preferential binding site for a quinone, designated QP, on the inner face of the encircling LH1 complex. Quinols, initially generated at the RC QB site, are proposed to transiently occupy the QP site prior to traversing the LH1 barrier and diffusing to the cytochrome bc1 complex. Thus, the QP site, which is analogous to other such sites in recent cryo-EM structures of RC-LH1 complexes, likely reflects a general mechanism for exporting quinols from the RC-LH1 complex.

Keywords: carotenoids; cryo-electron microscopy; light-harvesting; photosynthesis; quinone; reaction centre.

Figure 1.. Cryo-EM structure of the RC–LH1 core complex from Rsp. rubrum.

(A–C) Views of the RC–LH1 density map, colored as in the key at the bottom of the figure. Detergent and other disordered molecules are in grey. (A) View of the slightly elliptical LH1 ring from the periplasmic side of the membrane, showing the diameters of the long and short axes. (B) View in the plane of the membrane showing the height of the complex. (C) Perpendicular view from the cytoplasmic side. (D–F) Ribbon models corresponding to (A–C), made using Chimera [58]; the LH1 subunits are numbered in (D).

Figure 2.. Protein–protein and protein–pigment interactions in the Rsp. rubrum RC–LH1 core complex.

(A) A single LH1 αβ subunit, containing one α-polypeptide (yellow), one β-polypeptide (cornflower blue), two BChl a_GG molecules colored according to their cognate polypeptide, and one all-trans spirilloxanthin (red-orange). All residues involved in H-bonds are labelled. (B) Inter-subunit interactions between three adjoining LH1 αβ subunits. Pigments are only shown in the middle subunit for clarity. Only residues involved in inter-subunit H-bonds are labelled.

Figure 3.. Arrangement of pigments and cofactors in the Rsp. rubrum RC–LH1 core complex.

(A) Perpendicular view from the periplasmic side of the membrane. Water molecules were omitted for clarity. PG, Phosphatidyl glycerol; CD, cardiolipin; SP, the reaction centre special pair of BChl a_GG molecules. (B) Location and pigment environment of the extra BChl a_GG (bright green; colours as in panel (A)). The central Mg ion of this BChl a_GG is coordinated by the nearby PG lipid molecule, indicated by a bright green arrow. A lone pair π interaction between Q_P and RC-L Leu 76 is indicated with a mauve arrow, and a mid-green arrow points to a lone pair π interaction between non-protein bound rhodoquinone RQ and the accessory BChl a_GG on the B-branch of the RC. (C) Detailed view of the bonding environment for the extra BChl a_GG (green). Three water molecules are shown as small red spheres, with hydrogen bonds shown as dashed lines with the distances in Ångstroms indicated. LH1 α is in yellow, The RC-H subunit is in cyan, and the PG is in magenta.

Figure 4.. Location of a quinone/quinol channel adjacent to the Q_P site in the LH1 ring.

(A) The RC–LH1 complex viewed from the periplasmic side, with α-helices represented as ribbons and appearing as circles in the case of LH1 polypeptides. Only quinone cofactors are shown. Subunits are colored as in Figure 1. LH1-αβ subunits 1, 5 and 6 are labeled. A green arrow indicates the proposed path taken by a quinol though the pore. (B) View of the LH1 complex in the plane of the membrane, from outside the complex. The LH1 α-polypeptide is in yellow, the β-polypeptide in cornflower blue, BChl a_GG molecules are blue, and the all-trans spirilloxanthin is in red-orange. The green dashed circle shows the pore, with the weak density of this particular GG tail allowing a view of the Q_P quinone (pink) visible in the background. (C) Densities of pigments adjacent to the LH1 pore. The grey ellipse delineates the weaker densities for the GG tail and the carotenoid at these positions in the LH1 ring.