PDBsum entry 1vf5

Photosynthesis

PDB id: 1vf5

Contents

Protein chains

202 a.a. *

138 a.a. *

286 a.a. *

168 a.a. *

32 a.a. *

33 a.a. *

23 a.a. *

27 a.a. *

35 a.a. *

27 a.a. *

Ligands

HEM ×8

TDS ×2

PL9 ×2

OPC ×4

CLA ×2

FES ×2

BCR ×2

Waters ×2

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.

Authors

G.Kurisu, H.Zhang, J.L.Smith, W.A.Cramer.

Ref.

Science, 2003, 302, 1009-1014. [DOI no: 10.1126/science.1090165]

PubMed id

14526088

Abstract

The cytochrome b6f complex provides the electronic connection between the photosystem I and photosystem II reaction centers of oxygenic photosynthesis and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis. A 3.0 angstrom crystal structure of the dimeric b6f complex from the thermophilic cyanobacterium Mastigocladus laminosus reveals a large quinone exchange cavity, stabilized by lipid, in which plastoquinone, a quinone-analog inhibitor, and a novel heme are bound. The core of the b6f complex is similar to the analogous respiratory cytochrome bc1 complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex.

Figure 3.
Fig. 3. Stereo views of the intramembrane core and bound molecules. (A) Side view. The two b hemes (gray) are bis-histidine-coordinated on the n and p sides of the B and D helices (blue). Chlorophyll a (green) is sandwiched between the F and G helices of subunit IV; the 20-carbon phytyl chain (green) extends normal to the figure into the p side of the quinone exchange cavity. Heme x (red-brown), ligated by water and the heme b[n] propionate, lines the quinone exchange cavity, in contact with plastoquinone (magenta) near the n side of the cavity. TDS (yellow) is near the p side. (B) Linkage and coordination of heme x. Colors are as in (A); Cys35 (yellow) on the n side of the A helix makes the single covalent thioether bond with heme x. The fifth ligand is a water that is hydrogen-bonded (dashed line) to a heme b[n] propionate. Phe^40, on the n side of the E helix, is parallel to heme x and near (6 to 9 Å) plastoquinone (PQ, magenta) in the cavity.

Figure 5.
Fig. 5. Hypothesis for pathway of electron transfer between ISP and cytochrome f. (A) Side views showing the cytochrome f and ISP extrinsic domains in the crystal structure (left) and the model in which the soluble domain of ISP is rotated by 25° toward cytochrome f (right). His26 and Leu27 (orange) are shown in a ball-and-stick model. Distances between Leu27 (cytochrome f) and His129 (ISP) are shown as dotted lines: 21 Å in the crystal structure and 5 Å in the model after 25° rotation. The rotational trajectory of the [2Fe-2S] cluster in the proposed model is shown as a dotted arrow. Color code is as in Fig. 2A. (B) Schematic drawing around the [2Fe-2S] cluster and cytochrome f heme, showing the distances in the experimental and model structures.

The above figures are reprinted by permission from the AAAs: Science (2003, 302, 1009-1014) copyright 2003.

Secondary reference #1

Title

A defined protein-Detergent-Lipid complex for crystallization of integral membrane proteins: the cytochrome b6f complex of oxygenic photosynthesis.

Authors

H.Zhang, G.Kurisu, J.L.Smith, W.A.Cramer.

Ref.

Proc Natl Acad Sci U S A, 2003, 100, 5160-5163. [DOI no: 10.1073/pnas.0931431100]

PubMed id

12702760

Figure 1.
Fig. 1. Schematic of cyt b[6]f complex in a membrane bilayer (a), a detergent micelle (b), and a detergent-lipid mixture (c). The 13 transmembrane helices predicted for the complex are shown, with cyt b[6] (pink) and subunit IV (yellow) having four and three transmembrane spans, respectively. In b, the greater conformational freedom of the subunits of the protein complex in the detergent micelle is depicted qualitatively by an exaggerated tilting of the -helices. The prediction of a more ordered ensemble of subunits in the presence of a low stoichiometry of lipid ( 10 per monomer) is shown. Red, lipid head group; green, detergent head group.

Figure 3.
Fig. 3. (a) A crystal of the cyt b[6]f complex from the cyanobacterium M. laminosus. The brownish nature relative to crystals of the cyt bc[1] complex (30-33) is derived from one molecule of chlorophyll a (18, 29) in the complex. (b) Difference spectra of cyt f (ascorbate minus ferricyanide) and cyt b[6] (dithionite minus ascorbate) in the cyt complex obtained from crystals.