Cryo-EM structure of the Blastochloris viridis LH1–RC complex at 2.9 Å

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The light-harvesting 1–reaction centre (LH1–RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the bacteriochlorophyll b-based LH1–RC complex from Blastochloris viridis that reveals the structural basis for absorption of infrared light and the molecular mechanism of quinone migration across the LH1 complex. The triple-ring LH1 complex comprises a circular array of 17 β-polypeptides sandwiched between 17 α- and 16 γ-polypeptides. Tight packing of the γ-apoproteins between β-polypeptides collectively interlocks and stabilizes the LH1 structure; this, together with the short Mg–Mg distances of bacteriochlorophyll b pairs, contributes to the large redshift of bacteriochlorophyll b absorption. The ‘missing’ 17th γ-polypeptide creates a pore in the LH1 ring, and an adjacent binding pocket provides a folding template for a quinone, Q P, which adopts a compact, export-ready conformation before passage through the pore and eventual diffusion to the cytochrome bc 1 complex.

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Fig. 1: Cryo-EM structure of the LH1–RC core complex from Blc. viridis.
Fig. 2: Pigment arrangement in the Blc. viridis LH1–RC core complex.
Fig. 3: Intra- and inter-subunit protein–protein and protein–pigment interactions.
Fig. 4: Interactions between the RC and the LH1 complex, and within the LH1 complex.
Fig. 5: A quinone–quinol channel in the LH1–RC core complex.

Change history

  • 05 April 2018

    The Extended Data Figures and Tables section originally published with this article was missing Table 1. This has now been corrected.


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C.N.H. and P.Q. acknowledge support from the Biotechnology and Biological Sciences Research Council (BBSRC) UK, award number BB/M000265/1, the European Research Council Advanced Award 338895 and the Sheffield University Imagine programme. C.N.H. was also partially supported by the Photosynthetic Antenna Research Center (PARC), an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences (Award number DE-SC0001035). D.P.C. acknowledges funding from the European Commission (Marie Skłodowska-Curie Global Fellowship 660652).

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Nature thanks R. Cogdell, R. A. Niederman and J. Rubinstein for their contribution to the peer review of this work.

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P.Q. and C.N.H. conceived the study. P.Q. and C.N.H. designed the experiments. P.Q., C.A.S., D.P.C. and P.W. performed the experiments. P.Q. analysed the results and generated structural models. P.Q. and C.N.H. wrote the paper.

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Correspondence to C. Neil Hunter.

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Extended data figures and tables

Extended Data Fig. 1 Absorption spectra of photosynthetic membranes and the purified LH1–RC core complex from Blc. viridis.

Absorption spectra of isolated membranes (dashed line) and the purified LH1–RC complex (solid line) were recorded at room temperature and normalized at their Q y bands at 1,015 nm and 1,008 nm. The peak at 831 nm together with a shoulder at ~970 nm arise from BChl b in the RC. Bacteriopheophytin appears as a poorly resolved peak at about 810 nm. The Q x bands give rise to a composite peak at 602 nm. The minor peak at about 558 nm arises from the cytochromes, the Soret band of which contributes in the approximately 410-nm region. Absorption features at 482, 450 and 420 nm correspond to carotenoids and the 399-nm maximum corresponds to the Soret band of BChl b in the core complex. No oxidized BChl b is observed which, if present, would cause an absorption peak at about 685 nm.

Extended Data Fig. 2 Residue–residue distance deviation between cryo-EM and X-ray structures of the RC from Blc. viridis.

a, Superposition of the X-ray structure (PDB: 1PRC, grey) and the cryo-EM structure (colour-coded as in Fig. 1) of the RC. A putative hinge point is indicated with a red dot. The bending direction of the cryo-EM structure is indicated with two green arrows. A red arrow points to a flexible RC-H loop. be, Residue–residue (RR) distance deviation maps 22 of the individual RC subunits C, M, L and H, respectively, comparing the structures from cryo-EM and X-ray crystallography (PDB: 1PRC) 21. Each vertical scale shows the standard deviation (s.d.) in Å. The flexible loop of RC-H is indicated with a red perpendicular arrow in e.

Extended Data Fig. 3 Cryo-EM densities and structural models of polypeptides and pigments in the Blc. viridis LH1–RC complex.

The colour code is the same as in Fig. 1. The contour levels of the density maps were adjusted to mirror their molecular weights.

Extended Data Fig. 4 Electron densities between and outside the LH1 and RC complexes, and local resolution maps of the LH1–RC core complex.

a, The LH1–RC complex as shown in Fig. 1f, but displayed at 70% transparency. Electron densities belonging to detergent, lipid and other disordered molecules are in grey. b, Side view of the core complex with the periplasmic side uppermost. c, View of the periplasmic side. All membrane-extrinsic parts of the complex were truncated for clarity. The coloured bar chart on the right shows the local structural resolution in Å.

Extended Data Fig. 5 Relationship between BChl a and BChl b Mg–Mg distances and Q y-band absorption in bacterial light harvesting complexes.

a, Correlation of Q y-band maximum and inter-subunit BChl a and BChl b Mg–Mg distances in five bacterial light-harvesting complexes. b, As in a, but for intra-subunit Mg–Mg distances. c, Values for the linear correlation coefficient R, calculated using least-squares linear regression ( n = 5 biologically independent samples in each case; one-sided significance test).

Extended Data Fig. 6 Structural comparisons of selected cofactors and details of the Q P binding site.

a, The LH1-B1008 BChl b pair from Blc. viridis (blue) compared with the LH1-B915 BChl a pair (green) from the X-ray structure of the Tch. tepidum LH1–RC complex (PDB: 3WMM). b, Comparison of the Q A menaquinone-9 (blue) from the cryo-EM model of the Blc. viridis LH1–RC with the Q A (green) from the X-ray structure of the Blc. viridis RC (PDB: 3T6E). c, As in b, but comparing Q B. d, The Q P binding site. Only LH1-α1 and part of RC-L are shown for clarity. Yellow, LH1-α1; orange, RC-L; blue, Q P; wheat, Q B. Amino acid residues making close contacts around Q P are numbered and listed accordingly.

Extended Data Fig. 7 Cryo-EM micrographs of the LH1–RC complex from Blc. viridis and calculation of the cryo-EM map resolution.

a, Protein particles embedded in vitrified ice. Examples of LH1–RC complexes are circled. 6,472 cryo-EM movies were recorded, from which 267,726 particles were picked manually for reference-free two-dimensional classification. During data processing, datasets of around 100,000 and around 167,000 particles were used independently for 3D reconstruction. They generated very similar 3D maps for the LH1–RC complex, so they were combined. b, The LH1–RC particles are covered by a thin layer of vitrified ice on a supported carbon film. Each image measures 393.2 × 406.8 nm. c, Gold-standard refinement was used for estimation of the final map resolution. The global resolution of 2.9 Å was calculated using an FSC cut off of 0.143.

Extended Data Fig. 8 Amino acid sequence of polypeptides in the LH1–RC complex from Blc. viridis.

Black, genome sequence; red, protein sequence; blue, missing in protein sequence.

Extended Data Fig. 9 Amino acid sequence alignment of LH1 α- and β-polypeptides in LH1–RC core complexes from purple photosynthetic bacteria.

All sequences have been aligned relative to the His residue that ligates BChls in the LH1 complexes. The α- and β-polypeptides of the P. molischianum LH2 complex are included for comparison. The sequence alignment was performed using CLUSTAL O v.1.2.4.

Extended Data Table 1 Cryo-EM data collection, refinement and validation statistics

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Qian, P., Siebert, C.A., Wang, P. et al. Cryo-EM structure of the Blastochloris viridis LH1–RC complex at 2.9 Å. Nature 556, 203–208 (2018).

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