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Cited by 85Complement system in diseasesLipid Membrane Structure and BehaviorBiomarkers in Disease Mechanisms

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Structural basis for membrane attack complex inhibition by CD59

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Couves, Emma C., Gardner, Scott, Voisin, Tomas B., Bickel, Jasmine K., Stansfeld, Phillip J., Tate, Edward W., Bubeck, Doryen·2023·Nature Communications
DOI 10.1038/s41467-023-36441-zPMC PMC9935631

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Abstract

CD59 is an abundant immuno-regulatory receptor that protects human cells from damage during complement activation. Here we show how the receptor binds complement proteins C8 and C9 at the membrane to prevent insertion and polymerization of membrane attack complex (MAC) pores. We present cryo-electron microscopy structures of two inhibited MAC precursors known as C5b8 and C5b9. We discover that in both complexes, CD59 binds the pore-forming β-hairpins of C8 to form an intermolecular β-sheet that prevents membrane perforation. While bound to C8, CD59 deflects the cascading C9 β-hairpins, rerouting their trajectory into the membrane. Preventing insertion of C9 restricts structural transitions of subsequent monomers and indirectly halts MAC polymerization. We combine our structural data with cellular assays and molecular dynamics simulations to explain how the membrane environment impacts the dual roles of CD59 in controlling pore formation of MAC, and as a target of bacterial virulence factors which hijack CD59 to lyse human cells.

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  1. Tomlinson, S., Taylor, P. W., Morgan, B. P. & Luzio, J. P. Killing of gram-negative bacteria by complement. Fractionation of cell membranes after complement C5b-9 deposition on to the surface of Salmonella minnesota Re595. Biochem J. 263, 505–511 (1989). · DOI
  2. Davies, A. et al. CD59, an LY-6-like protein expressed in human lymphoid cells, regulates the action of the complement membrane attack complex on homologous cells. J. Exp. Med. 170, 637–654 (1989). · DOI
  3. Nevo, Y. et al. CD59 deficiency is associated with chronic hemolysis and childhood relapsing immune-mediated polyneuropathy. Blood 121, 129–135 (2013). · DOI
  4. Fishelson, Z., Donin, N., Zell, S., Schultz, S. & Kirschfink, M. Obstacles to cancer immunotherapy: expression of membrane complement regulatory proteins (mCRPs) in tumors. Mol. Immunol. 40, 109–123 (2003). · DOI
  5. Shao, F. et al. Silencing EGFR-upregulated expression of CD55 and CD59 activates the complement system and sensitizes lung cancer to checkpoint blockade. Nat. Cancer 3, 1192–1210 (2022). · DOI
  6. Podack, E. R. Molecular composition of the tubular structure of the membrane attack complex of complement. J. Biol. Chem. 259, 8641–8647 (1984). · DOI
  7. Ninomiya, H. & Sims, P. J. The human complement regulatory protein CD59 binds to the alpha-chain of C8 and to the “b“domain of C9. J. Biol. Chem. 267, 13675–13680 (1992). · DOI
  8. Huang, Y., Qiao, F., Abagyan, R., Hazard, S. & Tomlinson, S. Defining the CD59-C9 binding interaction. J. Biol. Chem. 281, 27398–27404 (2006). · DOI
  9. Bodian, D. L., Davis, S. J., Morgan, B. P. & Rushmere, N. K. Mutational analysis of the active site and antibody epitopes of the complement-inhibitory glycoprotein, CD59. J. Exp. Med 185, 507–516 (1997). · DOI
  10. Lockert, D. H. et al. Identity of the segment of human complement C8 recognized by complement regulatory protein CD59. J. Biol. Chem. 270, 19723–19728 (1995). · DOI
  11. Law, R. H. et al. The structural basis for membrane binding and pore formation by lymphocyte perforin. Nature 468, 447–451 (2010). · DOI
  12. Rosado, C. J. et al. A common fold mediates vertebrate defense and bacterial attack. Science 317, 1548–1551 (2007). · DOI
  13. Shatursky, O. et al. The mechanism of membrane insertion for a cholesterol-dependent cytolysin: a novel paradigm for pore-forming toxins. Cell 99, 293–299 (1999). · DOI
  14. Serna, M., Giles, J. L., Morgan, B. P. & Bubeck, D. Structural basis of complement membrane attack complex formation. Nat. Commun. 7, 10587 (2016). · DOI
  15. Spicer, B. A. et al. The first transmembrane region of complement component-9 acts as a brake on its self-assembly. Nat. Commun. 9, 3266 (2018). · DOI
  16. Hadders, M. A., Beringer, D. X. & Gros, P. Structure of C8alpha-MACPF reveals mechanism of membrane attack in complement immune defense. Science 317, 1552–1554 (2007). · DOI
  17. Lovelace, L. L., Cooper, C. L., Sodetz, J. M. & Lebioda, L. Structure of human C8 protein provides mechanistic insight into membrane pore formation by complement. J. Biol. Chem. 286, 17585–17592 (2011). · DOI
  18. Giddings, K. S., Zhao, J., Sims, P. J. & Tweten, R. K. Human CD59 is a receptor for the cholesterol-dependent cytolysin intermedilysin. Nat. Struct. Mol. Biol. 11, 1173–1178 (2004). · DOI
  19. Wickham, S. E. et al. Mapping the intermedilysin-human CD59 receptor interface reveals a deep correspondence with the binding site on CD59 for complement binding proteins C8alpha and C9. J. Biol. Chem. 286, 20952–20962 (2011). · DOI
  20. Johnson, S., Brooks, N. J., Smith, R. A., Lea, S. M. & Bubeck, D. Structural basis for recognition of the pore-forming toxin intermedilysin by human complement receptor CD59. Cell Rep. 3, 1369–1377 (2013). · DOI
  21. Farkas, I. et al. CD59 blocks not only the insertion of C9 into MAC but inhibits ion channel formation by homologous C5b-8 as well as C5b-9. J. Physiol. 539, 537–545 (2002). · DOI
  22. Meri, S. et al. Human protectin (CD59), an 18,000–20,000 MW complement lysis restricting factor, inhibits C5b-8 catalysed insertion of C9 into lipid bilayers. Immunology 71, 1–9 (1990).
  23. Hill, A. et al. Protection of erythrocytes from human complement-mediated lysis by membrane-targeted recombinant soluble CD59: a new approach to PNH therapy. Blood 107, 2131–2137 (2006). · DOI
  24. Kastner, B. et al. GraFix: sample preparation for single-particle electron cryomicroscopy. Nat. Methods 5, 53–55 (2008). · DOI
  25. Ng, S. C., Rao, A. G., Howard, O. M. & Sodetz, J. M. The eighth component of human complement: evidence that it is an oligomeric serum protein assembled from products of three different genes. Biochemistry 26, 5229–5233 (1987). · DOI
  26. Steckel, E. W., Welbaum, B. E. & Sodetz, J. M. Evidence of direct insertion of terminal complement proteins into cell membrane bilayers during cytolysis. Labeling by a photosensitive membrane probe reveals a major role for the eighth and ninth components. J. Biol. Chem. 258, 4318–4324 (1983). · DOI
  27. Menny, A. et al. Structural basis of soluble membrane attack complex packaging for clearance. Nat. Commun. 12, 6086 (2021). · DOI
  28. Leath, K. J. et al. High-resolution structures of bacterially expressed soluble human CD59. Acta Crystallogr Sect. F. Struct. Biol. Cryst. Commun. 63, 648–652 (2007). · DOI
  29. Menny, A. et al. CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers. Nat. Commun. 9, 5316 (2018). · DOI
  30. Petranka, J. et al. Structure-function relationships of the complement regulatory protein, CD59. Blood Cells Mol. Dis. 22, 281–296 (1996). · DOI
  31. Rollins, S. A., Zhao, J., Ninomiya, H. & Sims, P. J. Inhibition of homologous complement by CD59 is mediated by a species-selective recognition conferred through binding to C8 within C5b-8 or C9 within C5b-9. J. Immunol. 146, 2345–2351 (1991). · DOI
  32. Lawrence, S. L. et al. Structural basis for receptor recognition by the human cd59-responsive cholesterol-dependent cytolysins. Structure 24, 1488–1498 (2016). · DOI
  33. Nakano, Y. et al. Determination of the active site of CD59 with synthetic peptides. Mol. Immunol. 32, 241–247 (1995). · DOI
  34. Suzuki, K. G. et al. Transient GPI-anchored protein homodimers are units for raft organization and function. Nat. Chem. Biol. 8, 774–783 (2012). · DOI
  35. Cragg, M. S. et al. Complement-mediated lysis by anti-CD20 mAb correlates with segregation into lipid rafts. Blood 101, 1045–1052 (2003). · DOI
  36. Cooper, N. R. & Müller-Eberhard, H. J. The reaction mechanism of human C5 in immune hemolysis. J. Exp. Med 132, 775–793 (1970). · DOI
  37. Parsons, E. S. et al. Single-molecule kinetics of pore assembly by the membrane attack complex. Nat. Commun. 10, 2066 (2019). · DOI
  38. Jiang, Y. et al. Membrane-mediated protein interactions drive membrane protein organization. Nat. Commun. 13, 7373 (2022). · DOI
  39. Koyama-Honda, I. et al. High-speed single-molecule imaging reveals signal transduction by induced transbilayer raft phases. J. Cell Biol. 219, e202006125 (2020). · DOI
  40. Polekhina, G., Giddings, K. S., Tweten, R. K. & Parker, M. W. Insights into the action of the superfamily of cholesterol-dependent cytolysins from studies of intermedilysin. Proc. Natl Acad. Sci. USA 102, 600–605 (2005). · DOI
  41. Shah, N. R. et al. Structural basis for tuning activity and membrane specificity of bacterial cytolysins. Nat. Commun. 11, 5818 (2020). · DOI
  42. Banerjee, P., Wehle, M., Lipowsky, R. & Santer, M. A molecular dynamics model for glycosylphosphatidyl-inositol anchors: “flop down” or “lollipop”? Phys. Chem. Chem. Phys. 20, 29314–29324 (2018). · DOI
  43. Giddings, K. S., Johnson, A. E. & Tweten, R. K. Redefining cholesterol’s role in the mechanism of the cholesterol-dependent cytolysins. Proc. Natl Acad. Sci. USA 100, 11315–11320 (2003). · DOI
  44. Cheerla, R. & Ayappa, K. G. Molecular dynamics study of lipid and cholesterol reorganization due to membrane binding and pore formation by listeriolysin O. J. Membr. Biol. 253, 535–550 (2020). · DOI
  45. Brandel, A. et al. The Gb3-enriched CD59/flotillin plasma membrane domain regulates host cell invasion by Pseudomonas aeruginosa. Cell Mol. Life Sci. 78, 3637–3656 (2021). · DOI
  46. Saifuddin, M. et al. Human immunodeficiency virus type 1 incorporates both glycosyl phosphatidylinositol-anchored CD55 and CD59 and integral membrane CD46 at levels that protect from complement-mediated destruction. J. Gen. Virol. 78, 1907–1911 (1997). · DOI
  47. Bavari, S. et al. Lipid raft microdomains: a gateway for compartmentalized trafficking of Ebola and Marburg viruses. J. Exp. Med 195, 593–602 (2002). · DOI
  48. Grinkova, Y. V., Denisov, I. G. & Sligar, S. G. Engineering extended membrane scaffold proteins for self-assembly of soluble nanoscale lipid bilayers. Protein Eng. Des. Sel. 23, 843–848 (2010). · DOI
  49. Fraser, D. A. et al. Generation of a recombinant, membrane-targeted form of the complement regulator CD59: activity in vitro and in vivo. J. Biol. Chem. 278, 48921–48927 (2003). · DOI
  50. Palovcak, E. et al. A simple and robust procedure for preparing graphene-oxide cryo-EM grids. J. Struct. Biol. 204, 80–84 (2018). · DOI
  51. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). · DOI
  52. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, e42166 (2018). · DOI
  53. Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016). · DOI
  54. Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019). · DOI
  55. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). · DOI · Paper page
  56. Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ 6, 5–17 (2019). · DOI
  57. Punjani, A. & Fleet, D. J. 3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J. Struct. Biol. 213, 107702 (2021). · DOI
  58. Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015). · DOI
  59. Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat. Methods 18, 176–185 (2021). · DOI
  60. Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D. Struct. Biol. 74, 519–530 (2018). · DOI
  61. Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D. Struct. Biol. 74, 531–544 (2018). · DOI
  62. Afonine, P. V. et al. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr D. Struct. Biol. 74, 814–840 (2018). · DOI
  63. Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46, W296–W303 (2018). · DOI
  64. Pettersen, E. F. et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021). · DOI
  65. Wu, E. L. et al. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J. Comput Chem. 35, 1997–2004 (2014). · DOI
  66. Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput Chem. 29, 1859–1865 (2008). · DOI · Paper page
  67. Brooks, B. R. et al. CHARMM: the biomolecular simulation program. J. Comput Chem. 30, 1545–1614 (2009). · DOI
  68. Lee, J. et al. CHARMM-GUI input generator for namd, gromacs, amber, openmm, and charmm/openmm simulations using the charmm36 additive force field. J. Chem. Theory Comput 12, 405–413 (2016). · DOI
  69. Fletcher, C. M., Harrison, R. A., Lachmann, P. J. & Neuhaus, D. Structure of a soluble, glycosylated form of the human complement regulatory protein CD59. Structure 2, 185–199 (1994). · DOI
  70. Jorgensen, W., Chandrasekhar, J. & Madura, J. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983). · DOI
  71. Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1-2, 19–25 (2015). · DOI · Paper page
  72. Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods 14, 71–73 (2017). · DOI
  73. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684 (1984). · DOI
  74. Periole, X., Cavalli, M., Marrink, S. J. & Ceruso, M. A. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics, and intermolecular recognition. J. Chem. Theory Comput 5, 2531–2543 (2009). · DOI
  75. Periole, X. & Marrink, S. J. The Martini coarse-grained force field. Methods Mol. Biol. 924, 533–565 (2013). · DOI
  76. Monticelli, L. et al. The MARTINI coarse-grained force field: extension to proteins. J. Chem. Theory Comput 4, 819–834 (2008). · DOI
  77. Banerjee, P., Lipowsky, R. & Santer, M. Coarse-grained molecular model for the glycosylphosphatidylinositol anchor with and without protein. J. Chem. Theory Comput 16, 3889–3903 (2020). · DOI
  78. Kirschner, K. N. et al. GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J. Comput Chem. 29, 622–655 (2008). · DOI
  79. Sousa da Silva, A. W. & Vranken, W. F. ACPYPE - AnteChamber PYthon Parser interfacE. BMC Res Notes 5, 367 (2012). · DOI
  80. Goga, N., Rzepiela, A. J., de Vries, A. H., Marrink, S. J. & Berendsen, H. J. Efficient algorithms for langevin and DPD dynamics. J. Chem. Theory Comput 8, 3637–3649 (2012). · DOI
  81. Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P. & de Vries, A. H. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 111, 7812–7824 (2007). · DOI
  82. Wassenaar, T. A., Ingólfsson, H. I., Böckmann, R. A., Tieleman, D. P. & Marrink, S. J. Computational lipidomics with insane: a versatile tool for generating custom membranes for molecular simulations. J. Chem. Theory Comput 11, 2144–2155 (2015). · DOI · Paper page
  83. Yesylevskyy, S. O., Schäfer, L. V., Sengupta, D. & Marrink, S. J. Polarizable water model for the coarse-grained MARTINI force field. PLoS Comput Biol. 6, e1000810 (2010). · DOI
  84. Essmann, U., Perera, L. & Berkowitz, M. L. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577 (1995). · DOI

Metadata

Authors
Couves, E. C., Gardner, S., Voisin, T. B., Bickel, J. K., Stansfeld, P. J., Tate, E. W., & Bubeck, D.
Affiliations
  • Imperial College London (GB)
  • University of Warwick (GB)
Corresponding author
Bubeck, Doryen
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-02-16
Volume
14
Issue
1
Pages
890-890
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-36441-z
PMC
PMC9935631
OpenAlex
W4321078922
Cited by
85
References
2
Citations by year
2026: 29 · 2025: 35 · 2024: 15 · 2023: 6
FWCI
9.32
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Warwick Research Archive Portal (University of Warwick) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Spiral (Imperial College London) (submittedVersion, other-oa)
  • Spiral (Imperial College London) (submittedVersion, cc-by-nc-nd)
Funders
  • Wellcome Trust (BB/S003339/1, Z/17/Z, 208361, 208361/Z/17/Z)
  • Francis Crick Institute
  • Diamond Light Source
  • Cancer Research UK (864751, EP/L015498/1, C24523/A26234, EP/R029407/1, A26234, C24523, BB/M011178/1)
  • Imperial College London (BB/M011178/1, A26234)
  • European Commission (HORIZON2020)
  • Medical Research Council (MR/S009213/1)
  • Engineering and Physical Sciences Research Council (EP/R029407/1, EP/R029407/2, 864751, R029407, EP/R029407, 1364172, BB/M011178/1, C24523/A26234, EP/L015498/1)
  • Biotechnology and Biological Sciences Research Council (BB/M011178/1, BB/R002517/1, EP/R029407/1, C24523/A26234, BB/S003339/1, BB/P01948X/1, BB/P01948X/2, P01948X, R002517, S003339, EP/L015498/1, 864751)
Topics
  • Life Sciences › Immunology and Microbiology › Immunology › Complement system in diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
  • Life Sciences › Immunology and Microbiology › Immunology › Biomarkers in Disease Mechanisms
Keywords
CD59, membrane attack complex, complement regulation, perfluorooctanoic acid, C9, beta-hairpin, intermolecular beta-sheet, membrane perforation, bacterial virulence factors, complement receptors, cryo-EM structure
MeSH terms
Complement Activation, Complement C8, Complement C9, Humans, Complement Membrane Attack Complex, CD59 Antigens, Cryoelectron Microscopy

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