Abstract
Target cell lysis is regulated by natural killer (NK) cell receptors that recognize class I MHC molecules. Here we report the crystal structure of the human immunoglobulin-like NK cell receptor KIR2DL2 in complex with its class I ligand HLA-Cw3 and peptide. KIR binds in a nearly orthogonal orientation across the α1 and α2 helices of Cw3 and directly contacts positions 7 and 8 of the peptide. No significant conformational changes in KIR occur on complex formation. The receptor footprint on HLA overlaps with but is distinct from that of the T-cell receptor. Charge complementarity dominates the KIR/HLA interface and mutations that disrupt interface salt bridges substantially diminish binding. Most contacts in the complex are between KIR and conserved HLA-C residues, but a hydrogen bond between Lys 44 of KIR2DL2 and Asn 80 of Cw3 confers the allotype specificity. KIR contact requires position 8 of the peptide to be a residue smaller than valine. A second KIR/HLA interface produced an ordered receptor–ligand aggregation in the crystal which may resemble receptor clustering during immune synapse formation.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
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
References
Biron, C. A., Nguyen, K. B., Pien, G. C., Cousens, L. P. & Salazar-Mather, T. P. Natural killer cells in antiviral defense: function and regulation by innate cytokines. Annu. Rev. Immunol. 17, 189–220 (1999).
Lanier, L. L. NK cell receptors. Annu. Rev. Immunol. 16, 359–393 (1998).
Lanier, L. L., Corliss, B. C., Wu, J., Leong, C. & Phillips, J. H. Immunoreceptor DAP12 bearing a tyrosine-based activation motif is invovled in activating NK cells. Nature 391 , 703–707 (1998).
Long, E. O. Regulation of immune responses through inhibitory receptors. Annu. Rev. Immunol. 17, 875–904 (1999).
Pende, D. et al. The susceptibility to natural killer cell-mediated lysis of HLA class I-positive melanomas reflects the expression of insufficient amounts of different HLA class I alleles. Eur. J. Immunol. 28, 2384–2394 (1998).
Fan, Q. R. et al. Structure of the inhibitory receptor for human natural killer cells resembles haematopoietic receptors. Nature 389 , 96–100 (1997).
Snyder, G. A., Brooks, A. G. & Sun, P. D. Crystal structure of the HLA-Cw3 allotype-specific killer cell inhibitory receptor KIR2DL2. Proc. Natl Acad. Sci. USA 96, 3864–3869 ( 1999).
Maenaka, K., Juji, T., Stuart, D. I. & Jones, E. Y. Crystal structure of the human p58 killer cell inhibitory receptor (KIR2DL3) specific for HLA-Cw3-related MHC class I. Structure 7, 391– 398 (1999).
Boyington, J. C. et al. Structure of CD94 reveals a novel C-type lectin fold: implications for the NK cell-associated CD94/NKG2 receptors. Immunity 10, 75–82 (1999).
Tormo, J., Natarajan, K., Margulies, D. H. & Mariuzza, R. A. Crystal structure of a lectin-like natural killer cell receptor bound to its MHC class I ligand. Nature 402, 623– 631 (1999).
Winter, C. C., Gumperz, J. E., Parham, P., Long, E. O. & Wagtmann, N. Direct binding and functional transfer of NK cell inhibitory receptors reveal novel patterns of HLA-C allotype recognition. J. Immunol. 161, 571–577 (1998).
Winter, C. C. & Long, E. O. A single amino acid in the p58 killer cell inhibitory receptor controls the ability of natural killer cells to discriminate between the two groups of HLA-C allotypes. J. Immunol. 158, 4026–4028 (1997).
Biassoni, R. et al. Role of amino acid position 70 in the binding affinity of p50.1 and p58.1 receptors for HLA-Cw4 molecules. Eur. J. Immunol. 27, 3095–3099 ( 1997).
Fan, Q R. & Wiley, D. C. Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor. J. Exp. Med. 190, 113– 123 (1999).
Lawrence, M. C. & Colman, P. M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946–950 (1993).
Ysern, X., Li, H. & Mariuzza, R. A. Imperfect interfaces. Nature Struct. Biol. 5, 412–414 ( 1998).
Wang, J. H. et al. Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors. Cell 97, 791–803 (1999).
Mandelboim, O. et al. The binding site of NK receptors on HLA-C molecules. Immunity 6, 341–350 ( 1997).
Zappacosta, F., Borrego, F., Brooks, A. G., Parker, K. C. & Coligan, J. E. Peptides isolated from HLA-Cw*0304 confer different degrees of protection from natural killer cell-mediated lysis. Proc. Natl Acad. Sci. USA 94, 6313– 6318 (1997).
Falk, K. et al. Allele-specific peptide ligand motifs of HLA-C molecules. Proc. Natl Acad. Sci. USA 90, 12005– 12009 (1993).
Garboczi, D. N. et al. Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature 384, 134– 141 (1996).
Rajagopalan, S. & Long, E. O. The direct binding of a p58 killer cell inhibitory receptor to human histocompatibility leukocyte antigen (HLA)-Cw4 exhibits peptide selectivity. J. Exp. Med. 185, 1523–1528 (1997).
Vales-Gomez, M., Reyburn, H. T., Erskine, R. A. & Strominger, J. Differential binding to HLA-C of p50-activating and p58-inhibitory natural killer cell receptors. Proc. Natl Acad. Sci. USA 95 , 14326–14331 (1998).
Maenaka, K. et al. Killer cell immunoglobulin receptors and T cell receptors bind peptide-major histocompatibility complex class I wiht distinct thermodynamic and kinetic properties. J. Biol. Chem. 274, 28329–28334 (1999).
Davis, S. J., Ikemizu, S., Wild, M. K. & van der Merwe, P. A. CD2 and the nature of protein interactions mediating cell-cell recognition. Immunol. Rev. 163, 217–236 (1998).
Colonna, M., Borsellino, G., Falco, M., Ferrara, G. B. & Strominger, J. L. HLA-C is the inhibitory ligand that determines dominant resistance to lysis by NK1- and NK2-specific natural killer cells. Proc. Natl Acad. Sci. USA 90, 12000–12004 (1993).
Mandelboim, O. et al. Protection from lysis by natural killer cells of group 1 and 2 specificity is mediated by residue 80 in human histocompatibility leukocyte antigen C alleles and also occurs with empty major histocompatibility complex molecules. J. Exp. Med. 184, 913– 922 (1996).
Barber, L. D. et al. The inter-locus recombinant HLA-B*4601 has high selectivity in peptide binding and functions characteristic of HLA-C. J. Exp. Med. 184, 735–740 ( 1996).
Peruzzi, M., Parker, K. C., Long, E. O. & Malnati, M. S. Peptide sequence requirements for the recognition of HLA-B*2705 by specific natural killer cells. J. Immunol. 157, 3350 –3356 (1996).
Rojo, S., Wagtmann, N. & Long, E. O. Binding of a soluble p70 killer cell inhibitory receptor to HLA-B*5101: requirement for all three p70 immunoglobulin domains. Eur. J. Immunol. 27, 568–571 (1997).
Littaua, R. A. et al. An HLA-C-restricted CD8+ cytoxic T-lymphocyte clone recognizes a highly conserved epitope on human immunodeficiency virus type 1 gag. J. Virol. 65, 4051–4056 (1991).
Hanke, T. et al. Direct assessment of MHC class I binding by seven Ly49 inhibitory NK cell receptors. Immunity 11, 67– 77 (1999).
Orihuela, M., Margulies, D. H. & Yokoyama, W. M. The natural killer cell receptor Ly-49A recognizes a peptide-induced conformational determinant on its major histocompatibility complex class I ligand. Proc. Natl Acad. Sci. USA 93 , 11792–11797 (1996).
Rajagopalan, S., Winter, C. C., Wagtmann, N. & Long, E. O. The Ig-related killer cell inhibitory receptor binds zinc and requires zinc for recognition of HLA-C on target cells. J. Immunol. 155, 4143–4146 (1995).
Davis, D. M. et al. The human natural killer cell immune synapse. Proc. Natl Acad. Sci. USA 96, 15062– 15067 (1999).
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 ( 1997).
Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163 ( 1994).
Brunger, A. T. et al. Crystallography & NMR system: A Software Suite for Macromolecular Structure Determination. Acta Crystallogr. D 54, 905–921 (1998).
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 the models. Acta Crystallogr. A 47, 110 –119 (1991).
The Collaborative Computing Project No. 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 ( 1995).
Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Applied Crystallography 24, 946–950 (1991).
Merrit, E. A. & Murphy, M. E. P. Raster 3D Version 2.0: a program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869–873 (1994).
Nicholls, A., Charp, 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).
Acknowledgements
We thank Z. Dauter and C. Titlow for help with synchrotron data collection; J. Lukszo for peptide synthesis; C. Hammer for mass spectroscopy measurements; M. Garfield for N-terminal amino-acid sequencing; A. Winterhalter and N. Mifsud for assistance with the mutagenesis and DNA sequencing; and D. Margulies for help with BIAcore SPR measurements. This work is supported by intramural research funding from the National Institute of Allergy and Infectious Diseases and an R. D. Wright Fellowship from the National Health and Medical Research Council, Australia.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Boyington, J., Motyka, S., Schuck, P. et al. Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand. Nature 405, 537–543 (2000). https://doi.org/10.1038/35014520
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/35014520
This article is cited by
-
Elevated KIR expression and diminished intensity of CD7 on NK cell subsets among treatment naïve HIV infected Ethiopians
Scientific Reports (2022)
-
Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C
Nature Communications (2021)
-
The microstructure in the placenta is influenced by the functional diversity of HLA-G allelic variants
Immunogenetics (2019)
-
Recognition of host Clr-b by the inhibitory NKR-P1B receptor provides a basis for missing-self recognition
Nature Communications (2018)
-
Specificity of inhibitory KIRs enables NK cells to detect changes in an altered peptide environment
Immunogenetics (2018)
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.