MHC-E regulates NK cells by displaying MHC class Ia signal peptides (VL9) to NKG2A:CD94 receptors. MHC-E can also present sequence-diverse, lower-affinity, pathogen-derived peptides to T cell receptors (TCRs) on CD8+ T cells. To understand these affinity differences, human MHC-E (HLA-E)-VL9 versus pathogen-derived peptide structures are compared. Small-angle X-ray scatter (SAXS) measures biophysical parameters in solution, allowing comparison with crystal structures. For HLA-E-VL9, there is concordance between SAXS and crystal parameters. In contrast, HLA-E-bound pathogen-derived peptides produce larger SAXS dimensions that reduce to their crystallographic dimensions only when excess peptide is supplied. Further crystallographic analysis demonstrates three amino acids, exclusive to MHC-E, that not only position VL9 close to the α2 helix, but also allow non-VL9 peptide binding with re-configuration of a key TCR-interacting α2 region. Thus, non-VL9-bound peptides introduce an alternative peptide-binding motif and surface recognition landscape, providing a likely basis for VL9- and non-VL9-HLA-E immune discrimination.

Department of Cell Biology Faculty of Science Charles University Prague Czech Republic

Department of Life Sciences and Chemistry Jacobs University Bremen Bremen Germany

Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK

Division of Structural Biology Wellcome Centre for Human Genetics University of Oxford Roosevelt Drive Oxford OX3 7BN UK

Institute of Immunology and Immunotherapy University of Birmingham Edgbaston Birmingham B15 2TT UK

Nuffield Department of Medicine Research Building Nuffield Department of Medicine University of Oxford Roosevelt Drive Oxford OX3 7FZ UK

Nuffield Department of Medicine Research Building Nuffield Department of Medicine University of Oxford Roosevelt Drive Oxford OX3 7FZ UK; Department of Laboratory Medicine The 1st Affiliated Hospital China Medical University Shenyang China

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Afonine P.V., Grosse-Kunstleve R.W., Echols N., Headd J.J., Moriarty N.W., Mustyakimov M., Terwilliger T.C., Urzhumtsev A., Zwart P.H., Adams P.D. Towards automated crystallographic structure refinement with phenix.refine. Acta. Crystallogr. D. Biol. Crystallogr. 2012;68:352–367. doi: 10.1107/S0907444912001308. PubMed DOI PMC

Anjanappa R., Garcia-Alai M., Kopicki J.D., Lockhauserbäumer J., Aboelmagd M., Hinrichs J., Nemtanu I.M., Uetrecht C., Zacharias M., Springer S., Meijers R. Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection. Nat. Commun. 2020;11:1314. doi: 10.1038/s41467-020-14862-4. PubMed DOI PMC

Bailey A., Dalchau N., Carter R., Emmott S., Phillips A., Werner J.M., Elliott T. Selector function of MHC I molecules is determined by protein plasticity. Sci. Rep. 2015;5:14928. doi: 10.1038/srep14928. PubMed DOI PMC

Birkinshaw R.W., Pellicci D.G., Cheng T.Y., Keller A.N., Sandoval-Romero M., Gras S., de Jong A., Uldrich A.P., Moody D.B., Godfrey D.I., Rossjohn J. αβ T cell antigen receptor recognition of CD1a presenting self lipid ligands. Nat. Immunol. 2015;16:258–266. doi: 10.1038/ni.3098. PubMed DOI PMC

Borbulevych O.Y., Piepenbrink K.H., Gloor B.E., Scott D.R., Sommese R.F., Cole D.K., Sewell A.K., Baker B.M. T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility. Immunity. 2009;31:885–896. doi: 10.1016/j.immuni.2009.11.003. PubMed DOI PMC

Borrego F., Ulbrecht M., Weiss E.H., Coligan J.E., Brooks A.G. Recognition of human histocompatibility leukocyte antigen (HLA)-E complexed with HLA class I signal sequence-derived peptides by CD94/NKG2 confers protection from natural killer cell-mediated lysis. J. Exp. Med. 1998;187:813–818. doi: 10.1084/jem.187.5.813. PubMed DOI PMC

Braud V., Yvonne Jones E., McMichael A. The human major histocompatibility complex class Ib molecule HLA-E binds signal sequence-derived peptides with primary anchor residues at positions 2 and 9. Eur. J. Immunol. 1997;27:1164–1169. doi: 10.1002/eji.1830270517. PubMed DOI

Braud V.M., Allan D.S.J., O'Callaghan C.A., Söderström K., D'Andrea A., Ogg G.S., Lazetic S., Young N.T., Bell J.I., Phillips J.H., et al. HLA-E binds to natural killer cell receptors CD94/NKG2A, B and C. Nature. 1998;391:795–799. doi: 10.1038/35869. PubMed DOI

Chen V.B., Arendall W.B., 3rd, Headd J.J., Keedy D.A., Immormino R.M., Kapral G.J., Murray L.W., Richardson J.S., Richardson D.C. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 2010;66:12–21. doi: 10.1107/S0907444909042073. PubMed DOI PMC

Cotton R.N., Shahine A., Rossjohn J., Moody D.B. Lipids hide or step aside for CD1-autoreactive T cell receptors. Curr. Opin. Immunol. 2018;52:93–99. doi: 10.1016/j.coi.2018.04.013. PubMed DOI PMC

Diamond Light Source (2022). Software for SAXS. https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/SAXS-Software.html.

Doorduijn E.M., Sluijter M., Querido B.J., Seidel U.J.E., Oliveira C.C., van der Burg S.H., van Hall T. T cells engaging the conserved MHC class Ib molecule qa-1(b) with TAP-independent peptides are semi-invariant lymphocytes. Front. Immunol. 2018;9:60. doi: 10.3389/fimmu.2018.00060. PubMed DOI PMC

Elliott T., Smith M., Driscoll P., McMichael A. Peptide selection by class I molecules of the major histocompatibility complex. Curr. Biol. 1993;3:854–866. doi: 10.1016/0960-9822(93)90219-e. PubMed DOI

Emsley P., Lohkamp B., Scott W.G., Cowtan K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 2010;66:486–501. doi: 10.1107/S0907444910007493. PubMed DOI PMC

Franke D., Svergun D.I. DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Crystallogr. 2009;42:342–346. doi: 10.1107/S0021889809000338. PubMed DOI PMC

Fremont D.H., Matsumura M., Stura E.A., Peterson P.A., Wilson l.A. Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb. Science. 1992;257:919–927. doi: 10.1126/science.1323877. PubMed DOI

Geraghty D.E., Stockschleader M., Ishitani A., Hansen J.A. Polymorphism at the HLA-E locus predates most HLA-A and -B polymorphism. Hum. Immunol. 1992;33:174–184. doi: 10.1016/0198-8859(92)90069-y. PubMed DOI

Grimsley C., Ober C. Population genetic studies of HLA-E: evidence for selection. Hum. Immunol. 1997;52:33–40. doi: 10.1016/S0198-8859(96)00241-8. PubMed DOI

Hansen S.G., Wu H.L., Burwitz B.J., Hughes C.M., Hammond K.B., Ventura A.B., Reed J.S., Gilbride R.M., Ainslie E., Morrow D.W., et al. Broadly targeted CD8(+) T cell responses restricted by major histocompatibility complex E. Science. 2016;351:714–720. doi: 10.1126/science.aac9475. PubMed DOI PMC

Harndahl M., Rasmussen M., Roder G., Dalgaard Pedersen I., Sørensen M., Nielsen M., Buus S. Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. Eur. J. Immunol. 2012;42:1405–1416. doi: 10.1002/eji.201141774. PubMed DOI

Hawse W.F., Gloor B.E., Ayres C.M., Kho K., Nuter E., Baker B.M. Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition. J. Biol. Chem. 2013;288:24372–24381. doi: 10.1074/jbc.M113.490664. PubMed DOI PMC

Hoare H.L., Sullivan L.C., Clements C.S., Ely L.K., Beddoe T., Henderson K.N., Lin J., Reid H.H., Brooks A.G., Rossjohn J. Subtle changes in peptide conformation profoundly affect recognition of the non-classical MHC class I molecule HLA-E by the CD94-NKG2 natural killer cell receptors. J. Mol. Biol. 2008;377:1297–1303. doi: 10.1016/j.jmb.2008.01.098. PubMed DOI

Joosten S.A., van Meijgaarden K.E., van Weeren P.C., Kazi F., Geluk A., Savage N.D.L., Drijfhout J.W., Flower D.R., Hanekom W.A., Klein M.R., Ottenhoff T.H.M. Mycobacterium tuberculosis peptides presented by HLA-E molecules are targets for human CD8+ T-cells with cytotoxic as well as regulatory activity. PLoS Pathog. 2010;6:e1000782. doi: 10.1371/journal.ppat.1000782. PubMed DOI PMC

Kaiser B.K., Barahmand-Pour F., Paulsene W., Medley S., Geraghty D.E., Strong R.K. Interactions between NKG2x immunoreceptors and HLA-E ligands display overlapping affinities and thermodynamics. J. Immunol. 2005;174:2878–2884. doi: 10.4049/jimmunol.174.5.2878. PubMed DOI

Kaiser B.K., Pizarro J.C., Kerns J., Strong R.K. Structural basis for NKG2A/CD94 recognition of HLA-E. Proc. Natl. Acad. Sci. USA. 2008;105:6696–6701. doi: 10.1073/pnas.0802736105. PubMed DOI PMC

Karplus P.A., Diederichs K. Linking crystallographic model and data quality. Science. 2012;336:1030–1033. doi: 10.1126/science.1218231. PubMed DOI PMC

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. 2000;164:6398–6405. doi: 10.4049/jimmunol.164.12.6398. PubMed DOI

Kikhney A.G., Svergun D.I. A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS. Lett. 2015;589:2570–2577. doi: 10.1016/j.febslet.2015.08.027. PubMed DOI

Kozin M.B., Svergun D.I. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 2001;34:33–41. doi: 10.1107/S0021889800014126. DOI

Krissinel E., Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D Biol. Crystallogr. 2004;60:2256–2268. doi: 10.1107/S0907444904026460. PubMed DOI

Krissinel E., Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 2007;372:774–797. doi: 10.1016/j.jmb.2007.05.022. PubMed DOI

Lee N., Goodlett D.R., Ishitani A., Marquardt H., Geraghty D.E., IshitAni A. HLA-E surface expression depends on binding of TAP-dependent peptides derived from certain HLA class I signal sequences. J. Immunol. 1998;160:4951–4960. PubMed

Lee N., Llano M., Carretero M., Ishitani A., Navarro F., López-Botet M., Geraghty D.E. HLA-E is a major ligand for the natural killer inhibitory receptor CD94/NKG2A. Proc. Natl. Acad. Sci. USA. 1998;95:5199–5204. doi: 10.1073/pnas.95.9.5199. PubMed DOI PMC

Malouli D., Hansen S.G., Hancock M.H., Hughes C.M., Ford J.C., Gilbride R.M., Ventura A.B., Morrow D., Randall K.T., Taher H., et al. Cytomegaloviral determinants of CD8(+) T cell programming and RhCMV/SIV vaccine efficacy. Sci. Immunol. 2021;6:eabg5413. doi: 10.1126/sciimmunol.abg5413. PubMed DOI PMC

Manalastas-Cantos K., Konarev P.V., Hajizadeh N.R., Kikhney A.G., Petoukhov M.V., Molodenskiy D.S., Panjkovich A., Mertens H.D.T., Gruzinov A., Borges C., et al. ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J Appl Crystallogr. 2021;54:343–355. PubMed PMC

McMurtrey C., Harriff M.J., Swarbrick G.M., Duncan A., Cansler M., Null M., Bardet W., Jackson K.W., Lewinsohn D.A., Hildebrand W., Lewinsohn D.M. T cell recognition of Mycobacterium tuberculosis peptides presented by HLA-E derived from infected human cells. PLoS One. 2017;12:e0188288. doi: 10.1371/journal.pone.0188288. PubMed DOI PMC

Murshudov G.N., Skubák P., Lebedev A.A., Pannu N.S., Steiner R.A., Nicholls R.A., Winn M.D., Long F., Vagin A.A. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 2011;67:355–367. doi: 10.1107/S0907444911001314. PubMed DOI PMC

O'Callaghan C.A., Tormo J., Willcox B.E., Braud V.M., Jakobsen B.K., Stuart D.I., McMichael A.J., Bell J.I., Jones E.Y. Structural features impose tight peptide binding specificity in the nonclassical MHC molecule HLA-E. Mol. Cell. 1998;1:531–541. doi: 10.1016/s1097-2765(00)80053-2. PubMed DOI

Petrie E.J., Clements C.S., Lin J., Sullivan L.C., Johnson D., Huyton T., Heroux A., Hoare H.L., Beddoe T., Reid H.H., et al. CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence. J. Exp. Med. 2008;205:725–735. doi: 10.1084/jem.20072525. PubMed DOI PMC

Prezzemolo T., van Meijgaarden K.E., Franken K.L., Caccamo N., Dieli F., Ottenhoff T.H.M., Joosten S.A. Detailed characterization of human Mycobacterium tuberculosis specific HLA-E restricted CD8(+) T cells. Eur. J. Immunol. 2018;48:293–305. doi: 10.1002/eji.201747184. PubMed DOI PMC

Reiser J.B., Legoux F., Gras S., Trudel E., Chouquet A., Léger A., Le Gorrec M., Machillot P., Bonneville M., Saulquin X., Housset D. Analysis of relationships between peptide/MHC structural features and naive T cell frequency in humans. J. Immunol. 2014;193:5816–5826. doi: 10.4049/jimmunol.1303084. PubMed DOI

Riley T.P., Hellman L.M., Gee M.H., Mendoza J.L., Alonso J.A., Foley K.C., Nishimura M.I., Vander Kooi C.W., Garcia K.C., Baker B.M. T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability. Nat. Chem. Biol. 2018;14:934–942. doi: 10.1038/s41589-018-0130-4. PubMed DOI PMC

Smith K.J., Reid S.W., Stuart D.I., McMichael A.J., Jones E.Y., Bell J.I. An altered position of the alpha 2 helix of MHC class I is revealed by the crystal structure of HLA-B∗3501. Immunity. 1996;4:203–213. doi: 10.1016/s1074-7613(00)80429-x. PubMed DOI

Strong R.K., Holmes M.A., Li P., Braun L., Lee N., Geraghty D.E. HLA-E allelic variants. J. Biol. Chem. 2003;278:5082–5090. doi: 10.1074/jbc.M208268200. PubMed DOI

Sullivan L.C., Clements C.S., Beddoe T., Johnson D., Hoare H.L., Lin J., Huyton T., Hopkins E.J., Reid H.H., Wilce M.C., et al. The heterodimeric assembly of the CD94-NKG2 receptor family and implications for human leukocyte antigen-E recognition. Immunity. 2007;27:900–911. doi: 10.1016/j.immuni.2007.10.013. PubMed DOI

Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 1999;76:2879–2886. doi: 10.1016/S0006-3495(99)77443-6. PubMed DOI PMC

Vagin A., Teplyakov A. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 2010;66:22–25. doi: 10.1107/S0907444909042589. PubMed DOI

van Bleek G.M., Nathenson S.G. The structure of the antigen-binding groove of major histocompatibility complex class I molecules determines specific selection of self-peptides. Proc. Natl. Acad. Sci. USA. 1991;88:11032–11036. doi: 10.1073/pnas.88.24.11032. PubMed DOI PMC

van Meijgaarden K.E., Haks M.C., Caccamo N., Dieli F., Ottenhoff T.H.M., Joosten S.A. Human CD8+ T-cells recognizing peptides from Mycobacterium tuberculosis (Mtb) presented by HLA-E have an unorthodox Th2-like, multifunctional, Mtb inhibitory phenotype and represent a novel human T-cell subset. PLoS Pathog. 2015;11:e1004671. doi: 10.1371/journal.ppat.1004671. PubMed DOI PMC

Vance R.E., Kraft J.R., Altman J.D., Jensen P.E., Raulet D.H. Mouse CD94/NKG2A is a natural killer cell receptor for the nonclassical major histocompatibility complex (MHC) class I molecule Qa-1(b) J. Exp. Med. 1998;188:1841–1848. doi: 10.1084/jem.188.10.1841. PubMed DOI PMC

Volkov V.V., Svergun D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 2003;36:860–864. doi: 10.1107/S0021889803000268. PubMed DOI PMC

Walters L.C., Harlos K., Brackenridge S., Rozbesky D., Barrett J.R., Jain V., Walter T.S., O'Callaghan C.A., Borrow P., Toebes M., et al. Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding. Nat. Commun. 2018;9:3137. doi: 10.1038/s41467-018-05459-z. PubMed DOI PMC

Walters L.C., McMichael A.J., Gillespie G.M. Detailed and atypical HLA-E peptide binding motifs revealed by a novel peptide exchange binding assay. Eur. J. Immunol. 2020;50:2075–2091. doi: 10.1002/eji.202048719. PubMed DOI

Winn M.D., Ballard C.C., Cowtan K.D., Dodson E.J., Emsley P., Evans P.R., Keegan R.M., Krissinel E.B., Leslie A.G.W., McCoy A., et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 2011;67:235–242. doi: 10.1107/S0907444910045749. PubMed DOI PMC

Wu H.L., Wiseman R.W., Hughes C.M., Webb G.M., Abdulhaqq S.A., Bimber B.N., Hammond K.B., Reed J.S., Gao L., Burwitz B.J., et al. The role of MHC-E in T cell immunity is conserved among humans, rhesus macaques, and cynomolgus macaques. J. Immunol. 2018;200:49–60. doi: 10.4049/jimmunol.1700841. PubMed DOI PMC

Wun K.S., Reijneveld J.F., Cheng T.Y., Ladell K., Uldrich A.P., Le Nours J., Miners K.L., McLaren J.E., Grant E.J., Haigh O.L., et al. T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids. Nat. Immunol. 2018;19:397–406. doi: 10.1038/s41590-018-0065-7. PubMed DOI PMC

Xu J., Baase W.A., Baldwin E., Matthews B.W. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein. Sci. 1998;7:158–177. doi: 10.1002/pro.5560070117. PubMed DOI PMC

Yanaka S., Ueno T., Shi Y., Qi J., Gao G.F., Tsumoto K., Sugase K. Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex. J. Biol. Chem. 2014;289:24680–24690. doi: 10.1074/jbc.M114.566174. PubMed DOI PMC