Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution

Abstract

The major light-harvesting complex of photosystem II (LHC-II) serves as the principal solar energy collector in the photosynthesis of green plants and presumably also functions in photoprotection under high-light conditions. Here we report the first X-ray structure of LHC-II in icosahedral proteoliposome assembly at atomic detail. One asymmetric unit of a large R32 unit cell contains ten LHC-II monomers. The 14 chlorophylls (Chl) in each monomer can be unambiguously distinguished as eight Chla and six Chlb molecules. Assignment of the orientation of the transition dipole moment of each chlorophyll has been achieved. All Chlb are located around the interface between adjacent monomers, and together with Chla they are the basis for efficient light harvesting. Four carotenoid-binding sites per monomer have been observed. The xanthophyll-cycle carotenoid at the monomer–monomer interface may be involved in the non-radiative dissipation of excessive energy, one of the photoprotective strategies that have evolved in plants.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Electron-density map at 2.72 Å resolution.
Figure 2: Organization and packing of the icosahedral particles.
Figure 3: Secondary structure of monomeric LHC-II apoprotein and trimerization.
Figure 4: Pigments in the LHC-II trimer and monomer.
Figure 5: Structure-based non-photochemical chlorophyll fluorescence quenching model in oligomeric LHC-II.

Similar content being viewed by others

References

  1. Peter, G. F. & Thornber, J. P. Biochemical composition and organization of higher plant photosystem II light-harvesting pigment-proteins. J. Biol. Chem. 266, 16745–16754 (1991)

    CAS  PubMed  Google Scholar 

  2. Ruban, A. V., Lee, P. J., Wentworth, M., Young, A. J. & Horton, P. Determination of the stoichiometry and strength of binding of xanthophylls to the photosystem II light harvesting complexes. J. Biol. Chem. 274, 10458–10465 (1999)

    Article  CAS  Google Scholar 

  3. Nußberger, S., Dörr, K., Wang, D. N. & Kühlbrandt, W. Lipid–protein interactions in crystals of plant light-harvesting complex. J. Mol. Biol. 234, 347–356 (1993)

    Article  Google Scholar 

  4. Horton, P., Ruban, A. V. & Walters, R. G. Regulation of light harvesting in green plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47, 655–684 (1996)

    Article  CAS  Google Scholar 

  5. Elrad, D., Niyogi, K. K. & Grossman, A. R. A major light-harvesting polypeptide of photosystem II functions in thermal dissipation. Plant Cell 14, 1801–1816 (2002)

    Article  CAS  Google Scholar 

  6. Nilsson, A. et al. Phosphorylation controls the three-dimensional structure of plant light harvesting complex II. J. Biol. Chem. 272, 18350–18357 (1997)

    Article  CAS  Google Scholar 

  7. Kühlbrandt, W., Wang, D. N. & Fujiyoshi, Y. Atomic model of plant light-harvesting complex by electron crystallography. Nature 367, 614–621 (1994)

    Article  ADS  Google Scholar 

  8. Michel, H. Crystallization of membrane proteins. Trends Biochem. Sci. 8, 56–59 (1983)

    Article  CAS  Google Scholar 

  9. Rossmann, M. G. in Methods in Macromolecular Crystallography (eds Turk, D. & Johnson, L.) 95–103 (IOS Press, Amsterdam, 2001)

    Google Scholar 

  10. Jordan, P. et al. Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution. Nature 411, 909–917 (2001)

    Article  ADS  CAS  Google Scholar 

  11. McLuskey, K., Prince, S. M., Cogdell, R. J. & Isaacs, N. W. The crystallographic structure of the B800–820 LH3 light-harvesting complex from the purple bacteria Rhodopseudomonas acidophila strain 7050. Biochemistry 40, 8783–8789 (2001)

    Article  CAS  Google Scholar 

  12. Bassi, R., Croce, R., Cugini, D. & Sandonà, D. Mutational analysis of a higher plant antenna protein provides identification of chromophores bound into multiple sites. Proc. Natl Acad. Sci. USA 96, 10056–10061 (1999)

    Article  ADS  CAS  Google Scholar 

  13. Remelli, R., Varotto, C., Sandonà, D., Croce, R. & Bassi, R. Chlorophyll binding to monomeric light-harvesting complex. A mutation analysis of chromophore-binding residues. J. Biol. Chem. 274, 33510–33521 (1999)

    Article  CAS  Google Scholar 

  14. Gradinaru, C. C. et al. The flow of excitation energy in LHCII monomers: implications for the structural model of the major plant antenna. Biophys. J. 75, 3064–3077 (1998)

    Article  ADS  CAS  Google Scholar 

  15. Bassi, R., Sandonà, D. & Croce, R. Novel aspects of chlorophyll a/b-binding proteins. Physiol. Planta. 100, 769–779 (1997)

    Article  CAS  Google Scholar 

  16. Plumley, F. G. & Schmidt, G. W. Reconstitution of chlorophyll a/b light-harvesting complexes: Xanthophyll-dependent assembly and energy transfer. Proc. Natl Acad. Sci. USA 84, 146–150 (1987)

    Article  ADS  CAS  Google Scholar 

  17. Croce, R., Weiss, S. & Bassi, R. Carotenoid-binding sites of the major light-harvesting complex II of higher plants. J. Biol. Chem. 274, 29613–29623 (1999)

    Article  CAS  Google Scholar 

  18. Paulsen, H., Finkenzeller, B. & Kuhlein, N. Pigments induce folding of light-harvesting chlorophyll a/b-binding protein. Eur. J. Biochem. 215, 809–816 (1993)

    Article  CAS  Google Scholar 

  19. Hobe, S., Niemeier, H., Bender, A. & Paulsen, H. Carotenoid binding sites in LHCIIb. Relative affinities towards major xanthophylls of higher plants. Eur. J. Biochem. 267, 616–624 (2000)

    Article  CAS  Google Scholar 

  20. Croce, R., Remelli, R., Varotto, C., Breton, J. & Bassi, R. The neoxanthin binding site of the major light harvesting complex (LHCII) from higher plants. FEBS Lett. 456, 1–6 (1999)

    Article  CAS  Google Scholar 

  21. Gradinaru, C. C., Stokkum, I. H. M. V., Pascal, A. A., Grondelle, R. V. & Amerongen, H. V. Identifying the pathways of energy transfer between carotenoids and chlorophylls in LHCII and CP29. A multicolor, femtosecond pump-probe study. J. Phys. Chem. B 104, 9330–9342 (2000)

    Article  CAS  Google Scholar 

  22. Croce, R., Müller, M. G., Bassi, R. & Holzwarth, A. R. Carotenoid-to-chlorophyll energy transfer in recombinant major light-harvesting complex (LHC-II) of higher plants. I. femtosecond transient absorption measurements. Biophys. J. 80, 901–915 (2001)

    Article  CAS  Google Scholar 

  23. Hieber, A. D., Bugos, R. C. & Yamamoto, H. Y. Plant lipocalins: violaxanthin de-epoxidase and zeaxanthin epoxidase. Biochim. Biophys. Acta 1482, 84–91 (2000)

    Article  CAS  Google Scholar 

  24. Demmig-Adams, B. & Adams, W. W. Photoprotection and other responses of plants to high light stress. Annu. Rev. Plant Physiol. Plant Mol. Biol. 43, 599–626 (1992)

    Article  CAS  Google Scholar 

  25. Gilmore, A. M. Mechanistic aspects of xanthophyll cycle-dependent photoprotection in higher plant chloroplasts and leaves. Physiol. Planta. 99, 197–209 (1997)

    Article  CAS  Google Scholar 

  26. Frank, H. A. et al. Photophysics of the carotenoids associated with the xanthophyll cycle in photosynthesis. Photosynth. Res. 41, 389–395 (1994)

    Article  CAS  Google Scholar 

  27. Ma, Y. Z., Holt, N. E., Li, X. P., Niyogi, K. K. & Fleming, G. R. Evidence for direct carotenoid involvement in the regulation of photosynthetic light harvesting. Proc. Natl Acad. Sci. USA 100, 4377–4382 (2003)

    Article  ADS  CAS  Google Scholar 

  28. Beddard, G. S., Carlin, S. E. & Porter, G. Concentration quenching of chlorophyll fluorescence in bilayer lipid vesicles and liposomes. Chem. Phys. Lett. 43, 27–32 (1976)

    Article  ADS  CAS  Google Scholar 

  29. Moya, I., Silvestri, M., Vallon, O., Cinque, G. & Bassi, R. Time-resolved fluorescence analysis of the photosystem II antenna proteins in detergent micelles and liposomes. Biochemistry 40, 12552–12561 (2001)

    Article  CAS  Google Scholar 

  30. Lou, S., Wang, K., Zhao, F., Xu, C. & Kuang, T. A comparative study on PS II light harvesting chlorophyll a/b protein complexes between spinach and cucumber. Acta Bot. Sin. 37, 192–197 (1995)

    CAS  Google Scholar 

  31. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    Article  CAS  Google Scholar 

  32. Tong, L. & Rossmann, M. G. The locked rotation function. Acta Crystallogr. A 46, 783–792 (1990)

    Article  Google Scholar 

  33. Weeks, C. M. & Miller, R. The design and implementation of SnB v2.0. J. Appl. Crystallogr. 32, 120–124 (1999)

    Article  CAS  Google Scholar 

  34. CCP4 Collaborative Computational Project, The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

    Article  Google Scholar 

  35. Jones, T. A. in Molecular Replacement (eds Dodson, E. J., Gover, S. & Wolf, W.) 92–105 (SERC Daresbury Laboratory, Warrington, 1992)

    Google Scholar 

  36. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  37. Mason, J. G. Nucleotide sequence of a cDNA encoding the light-harvesting chlorophyll a/b binding protein from spinach. Nucleic Acids Res. 17, 5387 (1989)

    Article  ADS  CAS  Google Scholar 

  38. Brünger, A. T. et al. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  Google Scholar 

  39. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993)

    Article  CAS  Google Scholar 

  40. Frishman, D. & Argos, P. Knowledge-based secondary structure assignment. Proteins Struct. Funct. Genet. 23, 566–579 (1995)

    Article  CAS  Google Scholar 

  41. Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991)

    Article  Google Scholar 

  42. Merritt, E. A. & Murphy, M. E. P. Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869–873 (1994)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank D. C. Liang and the late P. S. Tang for their efforts in initiating this project; X. C. Gu for discussions; N. Sakabe and K. Sakabe at PF (Tsukuba, Japan) and the staff at BSRF (Beijing, China) for their support during data collection at the synchrotron facilities. This research was financially supported by the National Key Research Development Project of China, the National Natural Science Foundation of China, the National Key Special Research Program and the Knowledge Innovation Program of the Chinese Academy of Sciences.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Wenrui Chang.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Tables

Supplementary Table 1: Coordinations of chlorophylls and their interactions with local environments; Supplementary Table 2: Interaction between chlorophylls with strong excitonic coupling; Supplementary Table 3: Interactions between carotenoids and chlorophylls. (DOC 74 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, Z., Yan, H., Wang, K. et al. Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution. Nature 428, 287–292 (2004). https://doi.org/10.1038/nature02373

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature02373

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing