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Structure of the LH1–RC complex from Thermochromatium tepidum at 3.0 Å

Nature volume 508, pages 228–232 (2014)Cite this article

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Abstract

The light-harvesting core antenna (LH1) and the reaction centre (RC) of purple photosynthetic bacteria form a supramolecular complex (LH1–RC) to use sunlight energy in a highly efficient manner. Here we report the first near-atomic structure, to our knowledge, of a LH1–RC complex, namely that of a Ca2+-bound complex from Thermochromatium tepidum, which reveals detailed information on the arrangement and interactions of the protein subunits and the cofactors. The RC is surrounded by 16 heterodimers of the LH1 αβ-subunit that form a completely closed structure. The Ca2+ ions are located at the periplasmic side of LH1. Thirty-two bacteriochlorophyll and 16 spirilloxanthin molecules in the LH1 ring form an elliptical assembly. The geometries of the pigment assembly involved in the absorption characteristics of the bacteriochlorophyll in LH1 and excitation energy transfer among the pigments are reported. In addition, possible ubiquinone channels in the closed LH1 complex are proposed based on the atomic structure.

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Figure 1: Architecture of the LH1–RC complex from T. tepidum.
Figure 2: Structural details of the LH1 ring.
Figure 3: Interactions between the LH1 and RC.
Figure 4: The pigment arrangement.
Figure 5: Channels in the LH1 ring.

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Protein Data Bank

Data deposits

The coordinates and structure factors for the P21 and C2 crystals have been deposited in the Protein Data Bank (http://www.pdb.org/pdb/home/home.do) under accession numbers 3WMN, 3WMO and 3WMM, respectively.

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Acknowledgements

We thank S. Takaichi for analysing the pigment compositions in LH1–RC and dry cells; F. Sekine for sequencing the genes encoding RC proteins; T. Nozawa for his support and interest at the initial stage; Y. Kimura, Masayuki Kobayashi and J.-R. Shen for their discussion; H. Suzuki, Dorina, M. Nakamura, F. Oh-hata and Miho Kobayashi for their contributions to the early stage of crystallization and data collection, and the Kao Corporation for kindly providing LDAO. This work was supported by a Grant-in-Aid for Scientific Research on the Priority Area “Structures of Biological Macromolecular Assemblies” and a Grant-in-Aid for Scientific Research (C) from the Ministry of Education, Culture, Sports, Science and Technology of Japan; by funds from the Takeda Science Foundation, the Kurata Memorial Hitachi Science and Technology Foundation (to Z.-Y.W.-O.), and the Targeted Proteins Research Program and the Photon and Quantum Basic Research Coordinated Development Program from the Ministry of Education, Culture, Sports, Science and Technology of Japan (to K.M.), and by a postdoctoral fellowship from Ibaraki University (to L.-J.Y.). This work was performed using the synchrotron beamline BL44XU at SPring-8 under the Cooperative Research Program of the Institute for Protein Research, Osaka University and the beamlines at the KEK Photon Factory. We are grateful to A. Nakagawa, E. Yamashita, N. Matsugaki and Y. Yamada for their assistance in the data collection.

Author information

Author notes

  1. Satomi Niwa, Long-Jiang Yu and Kazuki Takeda: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan,

    Satomi Niwa, Kazuki Takeda, Yu Hirano & Kunio Miki

  2. Faculty of Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan,

    Long-Jiang Yu, Tomoaki Kawakami & Zheng-Yu Wang-Otomo

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  1. Satomi Niwa
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Contributions

Z.-Y.W.-O. and K.M. initiated the project and supervised all experiments. L.-J.Y. carried out experiments of purification, crystallization and post-crystallization treatment. Y.H. conducted screenings of crystallization condition. L.-J.Y., Y.H. and T.K. collected X-ray diffraction data. S.N. and K.T. carried out structure determination. All authors contributed to the data analysis. S.N., K.T., L.-J.Y., Z.-Y.W.-O. and K.M. prepared the manuscript. All authors approved the final version of the manuscript.

Corresponding authors

Correspondence to Zheng-Yu Wang-Otomo or Kunio Miki.

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Extended data figures and tables

Extended Data Figure 1 Crystal packing of the LH1–RC complex.

a, The LH1–RC complexes in the crystal lattice of the P21 crystals are shown as ribbons. Molecules in the asymmetric unit are coloured in blue and light blue, whereas symmetry-related molecules are in grey. The unit cell boundaries are defined by red lines. b, The LH1–RC complexes in the crystal lattice of the C2 crystals are shown as ribbons. A molecule in the asymmetric unit is coloured in blue, whereas symmetry-related molecules are in grey.

Extended Data Figure 2 Close-up views of the electron density maps of the LH1–RC complex.

a–d, The experimental (left) and sigmaA-weighted 2Fobs − Fcalc (right) electron density maps for the transmembrane regions of RC (a) and LH1 (b), the special-pair BChls (c) and the ubiquinone molecule (d) are represented as grey meshes. The contour levels are 1.0σ except the experimental maps of c and d contoured at 0.8σ.

Extended Data Figure 3 Primary and three-dimensional structure of the RC from T. tepidum.

a, Full amino acid sequences of the T. tepidum RC proteins deduced from the re-verified nucleotide sequences of puf operon and puhA. Red shaded letters denote the corrected amino acid residues that are different from those reported previously. The letters coloured in grey denote the amino acid residues that are not visible in the electron density map. b, Comparison of the RC structures from T. tepidum. The RC in the isolated state (grey) and the RC in the LH1–RC complex (red) are superimposed. c, The most deviated portion (residues 172–196 in Cyt subunit).

Extended Data Figure 4 Anomalous diffraction signals.

a, Anomalous difference Fourier maps calculated from the data sets collected at 2.70 Å (higher energy than the K-edge of calcium) are represented as meshes in red (5σ) and pink (3σ) for the LH1–RC structure. b, A close-up view for the calcium ion located on the interface of the Cyt and M subunits at contour levels of 5σ. c, A close-up view for a calcium ion located in the LH1 at contour levels of 5σ. d, Anomalous difference Fourier maps at 3.15 Å (lower energy than the K-edge of calcium) are represented in pink at contour levels of 3σ.

Extended Data Figure 5 Sequences of α- and β-apoproteins.

a, Sequence alignment for the α-apoproteins. Fully, highly and relatively conserved residues are shaded by red, light red and pale red, respectively. The helices for the α-apoprotein of T. tepidum are represented as blue cylinders and the loops are represented as yellow lines. Unmodelled regions are represented as grey dotted lines. The purple and pink triangles indicate the coordinating residues to magnesium and calcium in the LH1 of T. tepidum, respectively. b, Sequence alignment for the β-apoproteins. The helix for the β-apoprotein of T. tepidum is represented as a green cylinder. c, Schematic representation of the α-apoprotein from T. tepidum. The filled circles in purple and pink indicate the residues coordinating to magnesium and calcium, respectively. d, Schematic representation of the β-apoprotein.

Extended Data Figure 6 Fluctuation of the extramembrane regions of the LH1.

a, The superimposition of all 16 αβ-heterodimers is shown in a stereo view. The α- and β-apoproteins are represented as blue and green tubes, respectively. The B915s are represented as purple sticks. b, The experimental (left) and sigmaA-weighted 2Fobs − Fcalc (right) electron density maps for the extramembrane regions of LH1. Main chains of the regions can be traced, whereas some side chains are difficult to observe. c, Thermal motion for Cα atoms of the LH1–RC complex are shown as thermal ellipsoids which are coloured according to the equivalent isotropic B-factors ranging from blue (smallest) to red (largest).

Extended Data Figure 7 Comparison with other antenna complexes.

a, An αβ-heterodimer of the T. tepidum LH1 (magenta) is compared with αβ-heterodimers of Rhodops. acidophila LH2 (blue). b, A view rotated by 90° from a around the vertical axis. c, An αβ-heterodimer of the LH1 of T. tepidum (magenta) is compared with αβ-heterodimers of LH2 from Rhodosp. molischianum (dark blue). d, A view rotated by 90° from c around the vertical axis. e, An αβ-heterodimer of the T. tepidum LH1 (magenta) is compared with αβ-heterodimers of Rhodops. acidophila LH3 (cyan). f, A view rotated by 90° from e around the vertical axis. g, Comparison of the ring structures of LH1 of T. tepidum (magenta) with the LH2 from Rhodosp. molischianum (dark blue), LH2 from Rhodops. acidophila (blue), and LH3 of Rhodops. acidophila (cyan). h, Comparison of the ring structure with Rhodops. palustris LH1–RC. The T. tepidum LH1–RC is coloured, whereas the complex from Rhodops. palustris is shown in grey and black (helix W).

Extended Data Figure 8 Variations in the inter-subunit spacing of LH1.

a, A cross section of the ring at the periplasmic (left panel) and cytoplasmic (right panel) ends of the transmembrane helices. Distances between the two neighbouring helices are indicated by the black lines connecting them. For the α-apoproteins, the distances are measured between the Cα atoms of the two neighbouring α-Val 39 at the periplasmic end and the two neighbouring α-Pro 17 at the cytoplasmic end. In a similar way, the distances are measured between the Cα atoms of the two neighbouring β-Ala 39 at the periplasmic end and the two neighbouring β-Phe 17 at the cytoplasmic end for the β-apoproteins. b, The putative quinone channels are viewed on a cross section of the molecular surface from the periplasmic side. The head groups of the ubiquinone molecule at the QB site are represented as red CPK models. c, Cross sections of two channels in the LH1 with different shapes are superimposed. The molecular envelopes of the widest and narrowest channels are represented in blue and pale red, respectively. The red arrow illustrates the diffusion route for the ubiquinones.

Extended Data Table 1 Data collection and refinement statistics
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Extended Data Table 2 Crystallographic statistics for derivative data sets
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Niwa, S., Yu, LJ., Takeda, K. et al. Structure of the LH1–RC complex from Thermochromatium tepidum at 3.0 Å. Nature 508, 228–232 (2014). https://doi.org/10.1038/nature13197

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