Crystal structure of CD1a in complex with a sulfatide self antigen at a resolution of 2.15 Å (original) (raw)

• Calabi, F., Jarvis, J.M., Martin, L. & Milstein, C. Two classes of CD1 genes. Eur. J. Immunol. 19, 285–292 (1989).
  Article CAS Google Scholar
• Kawano, T. et al. CD1d-restricted and TCR-mediated activation of vα14 NKT cells by glycosylceramides. Science 278, 1626–1629 (1997).
  Article CAS Google Scholar
• Beckman, E.M. et al. CD1c restricts responses of mycobacteria-specific T cells. Evidence for antigen presentation by a second member of the human CD1 family. J. Immunol. 157, 2795–2803 (1996).
  CAS Google Scholar
• Porcelli, S., Morita, C.T. & Brenner, M.B. CD1b restricts the response of human CD4-8-T lymphocytes to a microbial antigen. Nature 360, 593–597 (1992).
  Article CAS Google Scholar
• Vincent, M.S. et al. CD1-dependent dendritic cell instruction. Nat. Immunol. 3, 1163–1168 (2002).
  Article CAS Google Scholar
• Rosat, J.P. et al. CD1-restricted microbial lipid antigen-specific recognition found in the CD8+ αβ T cell pool. J. Immunol. 162, 366–371 (1999).
  CAS Google Scholar
• Moody, D.B. et al. Structural requirements for glycolipid antigen recognition by CD1b-restricted T cells. Science 278, 283–286 (1997).
  Article CAS Google Scholar
• Shamshiev, A. et al. Self glycolipids as T-cell autoantigens. Eur. J. Immunol. 29, 1667–1675 (1999).
  Article CAS Google Scholar
• Shamshiev, A. et al. Presentation of the same glycolipid by different CD1 molecules. J. Exp. Med. 195, 1013–1021 (2002).
  Article CAS Google Scholar
• Moody, D.B. et al. CD1c-mediated T-cell recognition of isoprenoid glycolipids in Mycobacterium tuberculosis infection. Nature 404, 884–888 (2000).
  Article CAS Google Scholar
• Beckman, E.M. et al. Recognition of a lipid antigen by CD1-restricted αβ+ T cells. Nature 372, 691–694 (1994).
  Article CAS Google Scholar
• Moody, D.B. & Porcelli, S.A. Intracellular pathways of CD1 antigen presentation. Nat. Rev. Immunol. 3, 11–22 (2003).
  Article CAS Google Scholar
• Sugita, M. et al. Separate pathways for antigen presentation by CD1 molecules. Immunity 11, 743–752 (1999).
  CAS Google Scholar
• Moody, D.B. et al. Lipid length controls antigen entry into endosomal and nonendosomal pathways for CD1b presentation. Nat. Immunol. 3, 435–442 (2002).
  Article CAS Google Scholar
• Jackman, R.M. et al. The tyrosine-containing cytoplasmic tail of CD1b is essential for its efficient presentation of bacterial lipid antigens. Immunity 8, 341–351 (1998).
  CAS Google Scholar
• Chiu, Y.H. et al. Distinct subsets of CD1d-restricted T cells recognize self-antigens loaded in different cellular compartments. J. Exp. Med. 189, 103–110 (1999).
  Article CAS Google Scholar
• Sugita, M., van Der Wel, N., Rogers, R.A., Peters, P.J. & Brenner, M.B. CD1c molecules broadly survey the endocytic system. Proc. Natl. Acad. Sci. USA 97, 8445–8450 (2000).
  Article CAS Google Scholar
• Sugita, M. et al. Failure of trafficking and antigen presentation by CD1 in AP-3- deficient cells. Immunity 16, 697–706 (2002).
  Article CAS Google Scholar
• Porcelli, S. et al. Recognition of cluster of differentiation 1 antigens by human CD4-CD8-cytolytic T lymphocytes. Nature 341, 447–450 (1989).
  Article CAS Google Scholar
• Zeng, Z. et al. Crystal structure of mouse CD1: an MHC-like fold with a large hydrophobic binding groove. Science 277, 339–345 (1997).
  Article CAS Google Scholar
• Gadola, S.D. et al. Structure of human CD1b with bound ligands at 2.3 Å, a maze for alkyl chains. Nat. Immunol. 3, 721–726 (2002).
  Article CAS Google Scholar
• Jackson, M.R., Song, E.S., Yang, Y. & Peterson, P.A. Empty and peptide-containing conformers of class I major histocompatibility complex molecules expressed in Drosophila melanogaster cells. Proc. Natl. Acad. Sci. USA 89, 12117–12121 (1992).
  Article CAS Google Scholar
• Matsumura, M., Saito, Y., Jackson, M.R., Song, E.S. & Peterson, P.A. In vitro peptide binding to soluble empty class I major histocompatibility complex molecules isolated from transfected Drosophila melanogaster cells. J. Biol. Chem. 267, 23589–23595 (1992).
  CAS PubMed Google Scholar
• Matsumura, M., Fremont, D.H., Peterson, P.A. & Wilson, I.A. Emerging principles for the recognition of peptide antigens by MHC class I molecules. Science 257, 927–934 (1992).
  Article CAS Google Scholar
• Madden, D.R. The three-dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 13, 587–622.(1995).
  Article CAS Google Scholar
• O×Brien, J.S., Fillerup, D.L. & Mead, J.F. Quantification and fatty acid and fatty aldehyde composition of ethanolamine, choline, and serine glycerophosphatides in human cerebral grey and white matter. J. Lipid. Res. 5, 329–338 (1964).
  Google Scholar
• Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281–296 (1991).
  Article CAS Google Scholar
• O'Callaghan, C.A. et al. Structural features impose tight peptide binding specificity in the nonclassical MHC molecule HLA-E. Mol. Cell. 1, 531–541 (1998).
  Article CAS Google Scholar
• Khan, A.R., Baker, B.M., Ghosh, P., Biddison, W.E. & Wiley, D.C. The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site. J. Immunol. 164, 6398–6405 (2000).
  Article CAS Google Scholar
• Speir, J.A., Abdel-Motal, U.M., Jondal, M. & Wilson, I.A. Crystal structure of an MHC class I presented glycopeptide that generates carbohydrate-specific CTL. Immunity 10, 51–61 (1999).
  Article CAS Google Scholar
• Lerche, M.H., Kragelund, B.B., Bech, L.M. & Poulsen, F.M. Barley lipid-transfer protein complexed with palmitoyl CoA: the structure reveals a hydrophobic binding site that can expand to fit both large and small lipid-like ligands. Structure 5, 291–306 (1997).
  Article CAS Google Scholar
• Young, A.C. et al. Structural studies on human muscle fatty acid binding protein at 1.4 Å resolution: binding interactions with three C18 fatty acids. Structure 2, 523–534 (1994).
  Article CAS Google Scholar
• Manolova, V., Hirabayashi, Y., Mori, L. & Libero, G.D. CD1a and CD1b surface expression is independent from de novo synthesized glycosphingolipids. Eur. J. Immunol. 33, 29–37 (2003).
  Article CAS Google Scholar
• Sidobre, S. & Kronenberg, M. CD1 tetramers: a powerful tool for the analysis of glycolipid-reactive T cells. J. Immunol. Methods 268, 107–121 (2002).
  Article CAS Google Scholar
• Otwinowski, Z. & Minor, W. HKL: Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
  Article CAS Google Scholar
• Vagin, A.A. & Teplyakov, A. MOLREP:an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022–1025 (1997).
  Article CAS Google Scholar
• Brünger, A.T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905–921 (1998).
  Google Scholar
• Pannu, N.S. & Read, R.J. Improved structure refinement through maximum likelyhood. Acta Crystallogr. A52, 659–668 (1996).
  Article CAS Google Scholar
• Brünger, A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472–475 (1992).
  Article Google Scholar
• Jones, T.A., Cowan, S., Zou, J.Y. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110–119 (1991).
  Article CAS Google Scholar
• Kleywegt, G.J. & Jones, T.A. Databases in protein crystallography. Acta Crystallogr. D54, 1119–1131 (1998).
  CAS Google Scholar
• Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum likelihood method. Acta Crystallogr. D53, 240–255 (1997).
  CAS Google Scholar
• CCP4. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).
• Winn, M.D., Isupov, M.N. & Murshudov, G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D57, 122–133 (2001).
  CAS Google Scholar
• 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
• Connolly, M.L. The molecular surface package. J. Mol. Graph. 11, 139–141 (1993).
  Article CAS Google Scholar
• Gelin, B.R. & Karplus, M. Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment. Biochemistry 18, 1256–1268 (1979).
  Article CAS Google Scholar
• Sheriff, S., Hendrickson, W.A. & Smith, J.L. Structure of myohemerythrin in the azidomet state at 1.7/1.3 Å resolution. J. Mol. Biol. 197, 273–296 (1987).
  Article CAS Google Scholar
• Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of proteins. J. Appl. Crystallogr. 24, 946–950 (1991).
  Article Google Scholar
• Merritt, E.A. & Bacon, D.J. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505–524 (1997).
  Article CAS Google Scholar
• Esnouf, R.M. An extensively modified version of Molscript that includes greatly enhanced coloring capabilities. J. Mol. Graph. Model. 15, 132–134 (1997).
  Article CAS Google Scholar
• Howlin, B., Butler, D.S., Moss, D.S., Harris, G.W. & Driessen, H.P.C. TLSANL: TLS parameter analysis program for segmented anisotropic refinement of macromolecular structures. J. Appl. Crystallogr. 26, 622–624 (1993).
  Article Google Scholar