PMC

Structure of Chlorophyll.
The structure of chlorophyll b is shown with International Union of Pure and Applied Chemistry numbering. In chlorophyll a, the C7 formyl is a methyl group. Chlorophyll a′ is the C13² epimer of chlorophyll a. The y axis of the molecule passes through the N atoms of rings A and C and the x axis through the N atoms of ring B and D. Without the central magnesium ion, the tetrapyrrole is referred to as a pheophytin.

Association of LHCI with PSI.
The complex is viewed along the membrane normal from the stromal side. The chlorophylls are shown as green planes with the central magnesium as a green sphere. Fe is shown as a red sphere and sulfur as a yellow sphere. The helices are shown as cylinders. The subunits of PSI are colored gray, with the exception that polypeptides novel to the plant PSI are colored pale red (top left of image) and PsaK is shown in blue and PsaF in yellow (see for a review of PSI polypeptides). The Lhca polypeptides are colored pale magenta (bottom of image). PyMOL was used to generate the image from coordinates provided by Adam Ben-Shem and Nathan Nelson ().

Cofactors in the b₆f Dimer.
The coordinates from the cyanobacterial structure were used to generate the figure (). The complex is viewed in dimeric form in the plane of the membrane with the lumen side on the bottom as in . Chlorophyll is shown in green, b hemes of cytochrome b₆ and the c-heme of cytochrome f in red, the novel heme in brown, and Fe and S as red and yellow balls, respectively. The Q_o site inhibitor, tridecyl stigmatellin, is shown in turquoise and a plastoquinone at the Q_i site in blue. One of the Rieske subunits is shaded as a dark gray to show the association of its cofactor-containing domain with the other monomer. The stromal side of the membrane is called the n-side in one work or the inside (i) in another, and the lumen side is called p-side or outside (o). has discussed the variety in nomenclature of cofactors and presentation of the complex.

Organization of Pigments in LHCII.
(A) The trimer is viewed along the membrane normal from the stromal side (left). The lumenal side (right) is viewed from the stromal side as if reflected in a mirror to facilitate visualization of chlorophyll proximities in the two layers. The color schemes of green for chlorophyll a, purple for chlorophyll b, the arbitrary numbering system for the pigments from 601 to 614, and representation of the chlorophylls as a line connecting two nitrogens of rings A and C with a central magnesium (see ), which emphasizes the direction of the Q_y axis, is retained from . The carotenoids are indicated in yellow for luteins, orange for neoxanthin, and magenta for the xanthophyll cycle pigment. As in , the pigments closer to the viewer appear darker than those further away. Hence, 24 chlorophylls are shown as dark planes in the stromal view. The lighter ones in that image are the ones in the lumen-side layer.
(B) The trimer is viewed in the plane of the membrane, perpendicular to the membrane normal as in . The red spheres show the negatively charged residues on the lumen side.

An Updated Z-Scheme Describing Photosynthetic Electron Transfer.
Each carrier is shown in both its oxidized and reduced form to facilitate the readers' understanding of the sequence of steps, in which each carrier accepts an electron from a donor to become reduced and is reoxidized as it gives an electron to an acceptor. The midpoint potentials of the carriers in this version of the scheme have been updated to reflect the recent literature but are yet only approximate, owing in part to artistic aesthetics and in part to the intrinsic difficulty of estimating these numbers. In the cytochrome b₆f complex (shown in pink to distinguish it as a heme-containing complex), the donor (reduced plastoquinol PQH₂) provides two electrons: one is transferred through the Rieske FeS protein and cytochrome f to plastocyanin (or cytochrome c₆) to photosystem I, while the other is transferred through the b-hemes to a bound quinone on the stromal side. The dashed arrow to and from PQH₂ distinguishes diffusion of the redox carrier from the solid arrows that signify electron transfer. The conversion from the ground to the excited state (indicated with an open vertical arrow) occurs upon absorption of a photon. Some of the carriers appear to have obscure names (e.g., Z in PSII and A₀ and A₁ in PSI) and these have a historical origin in that the carriers had been identified as spectroscopic signals long before their chemical identities were known. In this scheme, A₀ is indicated as Chl and A₁ as PhQ to lead the reader away from obscurity. have suggested a specific nomenclature for the electron transfer cofactors in PSI.

Cofactors in PSII.
The cofactors in PSII, based on Protein Data Bank coordinates 1S5L, are shown. The view is perpendicular to the membrane normal. The color scheme of is retained. Chlorophylls are indicated in green, with the central Mg shown as a black sphere. The core antenna chlorophylls are distinguished from reaction center chlorophylls by the use of planes lacking phytol tails for the former versus sticks for the latter. P_D1 and P_D2 are in darker green to distinguish them from Chl_D1 and Chl_D2. Heme in cytochrome b₅₅₉ is diagrammed in pale-red sticks, carotenoids in orange, pheophytin in blue, and plastoquinone in pink. The tail of plastoquinone is omitted for clarity. The metals are shown as spheres: red for iron, magenta for manganese, and cyan for calcium. The side chains of Tyr161 (Y_Z) and His190 near the Mn₄Ca cluster are shown as gray sticks for carbon, blue for nitrogen, and red for oxygen. The inset shows an enlargement of the Mn₄Ca cluster as proposed by , with Y_Z on the top left and His190 on the bottom right. Two waters and a hydrogen on Tyr_Z are modeled as per . Note that there is considerable ambiguity concerning the structure of the cluster (see main text). The subscripts D1 and D2 denote the polypeptide binding site of the cofactor. The polypeptide nomenclature is historical: D1 and D2 for the apoproteins that bind most of the cofactors in PSII are so named because they had been initially revealed as diffuse staining bands in thylakoid membrane preparations. CP43 and CP47 stand for chlorophyll-protein, with the numbers indicating their size as estimated from SDS-PAGE. The heme binding heterodimer is called cytochrome b₅₅₉, reflecting the absorption maximum of the α band of the heme group, and other proteins are named as gene products (Psb_). PyMOL was used to generate this and other images. In all images, molecules closer to the reader are colored in a deeper shade, while those that are more distant are in a paler shade.