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Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36

Nature volume 504, pages 172–176 (2013)Cite this article

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Abstract

Members of the CD36 superfamily of scavenger receptor proteins are important regulators of lipid metabolism and innate immunity. They recognize normal and modified lipoproteins, as well as pathogen-associated molecular patterns. The family consists of three members: SR-BI (which delivers cholesterol to the liver and steroidogenic organs and is a co-receptor for hepatitis C virus), LIMP-2/LGP85 (which mediates lysosomal delivery of β-glucocerebrosidase and serves as a receptor for enterovirus 71 and coxsackieviruses) and CD36 (a fatty-acid transporter and receptor for phagocytosis of effete cells and Plasmodium-infected erythrocytes). Notably, CD36 is also a receptor for modified lipoproteins and β-amyloid, and has been implicated in the pathogenesis of atherosclerosis and of Alzheimer’s disease1. Despite their prominent roles in health and disease, understanding the function and abnormalities of the CD36 family members has been hampered by the paucity of information about their structure. Here we determine the crystal structure of LIMP-2 and infer, by homology modelling, the structure of SR-BI and CD36. LIMP-2 shows a helical bundle where β-glucocerebrosidase binds, and where ligands are most likely to bind to SR-BI and CD36. Remarkably, the crystal structure also shows the existence of a large cavity that traverses the entire length of the molecule. Mutagenesis of SR-BI indicates that the cavity serves as a tunnel through which cholesterol(esters) are delivered from the bound lipoprotein to the outer leaflet of the plasma membrane. We provide evidence supporting a model2 whereby lipidic constituents of the ligands attached to the receptor surface are handed off to the membrane through the tunnel, accounting for the selective lipid transfer characteristic of SR-BI and CD36.

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Figure 1: Structure of the human LIMP-2 luminal domain.
Figure 2: The helical bundle face and the apex region of LIMP-2 are required for association with β-GCase.
Figure 3: SR-BI and CD36 use the same interface as LIMP-2 for ligand binding.
Figure 4: SR-BI has a functionally important tunnel.

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Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited in Protein Data Bank under accession number 4F7B.

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Acknowledgements

We thank W. Temple, D. Cossar, S. Graslund, C. Arrowsmith, R. Stahelin, L. Andresen, J. Groth, M. Langer and J. Scott for assistance and discussions. This study was supported by the Canadian Institutes for Health Research (grants MOP-102474 and MOP-126069) and the Deutsche Forschungsgemeinschaft (grants GRK1459 to M.S. and SFB877). F.Z. is supported through the Böhringer Ingelheim Fonds. W.S.T. is the recipient of a Canada Research Chair in Molecular Cell Biology. The Structural Genomics Consortium is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research, the Canada Foundation for Innovation, Genome Canada through the Ontario Genomics Institute, GlaxoSmithKline, Karolinska Institutet, the Knut and Alice Wallenberg Foundation, the Ontario Innovation Trust, the Ontario Ministry for Research and Innovation, Merck & Co., the Novartis Research Foundation, the Swedish Agency for Innovation Systems, the Swedish Foundation for Strategic Research, and the Wellcome Trust. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Authors and Affiliations

  1. Cell Biology Program, The Hospital for Sick Children, Toronto M5G 1X8, Canada,

    Dante Neculai, Richard F. Collins, Jonathan Plumb, William S. Trimble & Sergio Grinstein

  2. Biochemisches Institut der Christian-Albrechts-Universität zu Kiel, Otto-Hahn-Platz 9, 24118 Kiel, Germany,

    Michael Schwake, Friederike Zunke, Judith Peters & Paul Saftig

  3. Biochemie III, Fakultät für Chemie, Universität Bielefeld, Universitätstrasse 25, 33615 Bielefeld, Germany,

    Michael Schwake

  4. Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada,

    Mani Ravichandran, Mirela Neculai, Peter Loppnau, Juan Carlos Pizarro, Alma Seitova & Sirano Dhe-Paganon

  5. Department of Tropical Medicine, Tulane University, New Orleans, 70118, Louisiana, USA

    Juan Carlos Pizarro

  6. Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada,

    William S. Trimble & Sergio Grinstein

  7. Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 209 Victoria Street, Toronto M5C 1N8, Canada,

    Sergio Grinstein

  8. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, 02215, Massachusetts, USA

    Sirano Dhe-Paganon

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  1. Dante Neculai
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Contributions

S.G., W.S.T., P.S., M.S., S.D.-P. and D.N. designed the research; D.N., M.R., M.N., P.L., A.S., J.C.P., R.C., J. Plumb, F.Z. and J. Peters performed the experiments; S.G., W.S.T., P.S., M.S., S.D.-P., D.N. and F.Z. analysed the results; S.G. wrote the paper; W.S.T., P.S., M.S., S.D.-P., D.N., J. Peters and F.Z. edited and commented on the manuscript.

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Correspondence to Sergio Grinstein.

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The authors declare no competing financial interests.

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Neculai, D., Schwake, M., Ravichandran, M. et al. Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36. Nature 504, 172–176 (2013). https://doi.org/10.1038/nature12684

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