Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote

Yueyong Xin,Yang Shi,Wei Ding,Tongxin Niu,Xiaoling Xu,Robert E Blankenship,Qingqiang Wang,Lei Yang,Xiaojun Huang,Fei Sun,Wanqiang Niu

doi:10.1038/s41467-018-03881-x

Abstract

Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC–LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery.

Highlights

Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC)
In the crystal structure of the purple sulfur bacterium Thermochromatium tepidum (T. tepidum) RC–LH1, it assembles into a closed elliptical LH ring, varied spaces between inter-LHαβ heterodimers were observed with a maximum of 2 Å between the α-helices on the periplasmic side and 3.5 Å on the cytoplasmic side[11]
We report the cryo-EM structure of the RC–LH core complex from R. castenholzii and observe a novel architecture with a gap in the LH ring, the insertion of a Cyt c transmembrane helix into the LH ring, and an unusual flexible helix TMx

Summary

Results

The whole rcRC–LH complex is 110 Å high; its transmembrane region is composed of an elliptical LH ring (averaged diameter of ~100 Å) and the TM helices of the L, M, and Cyt c subunits (Fig. 1a). Instead of a menaquinone and a ubiquinone as found in many purple bacteria[29], two menaquinone-11 (QA and QB) were resolved in the quinone-binding pockets of the L and M subunits at the cytoplasmic side (Fig. 2c), respectively, according to the density map (Supplementary Fig. 5I) as well as previous biochemical studies[22]. Superimposition of Cyt c subunit from rcRC–LH with that of ttRC–LH1 showed that, except for the N-terminal region, the five α helices (H1–H5) that coordinate four heme molecules on the periplasmic side can be overlaid very well (Fig. 2f). The angles between the transmembrane helices of LHα and LHβ within a LHαβ heterodimer are all bigger in rcRC–LH than in ttRC–LH1 (Supplementary Table 6). The architecture of rpRC–LH1 shows a gap, but the gap locates at the position of the 1st LHαβ (Fig. 4a)

H M-TM5 M-TM2

Discussion

Methods