Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Structural basis for ligand reception by anaplastic lymphoma kinase


The proto-oncogene ALK encodes anaplastic lymphoma kinase, a receptor tyrosine kinase that is expressed primarily in the developing nervous system. After development, ALK activity is associated with learning and memory1 and controls energy expenditure, and inhibition of ALK can prevent diet-induced obesity2. Aberrant ALK signalling causes numerous cancers3. In particular, full-length ALK is an important driver in paediatric neuroblastoma4,5, in which it is either mutated6 or activated by ligand7. Here we report crystal structures of the extracellular glycine-rich domain (GRD) of ALK, which regulates receptor activity by binding to activating peptides8,9. Fusing the ALK GRD to its ligand enabled us to capture a dimeric receptor complex that reveals how ALK responds to its regulatory ligands. We show that repetitive glycines in the GRD form rigid helices that separate the major ligand-binding site from a distal polyglycine extension loop (PXL) that mediates ALK dimerization. The PXL of one receptor acts as a sensor for the complex by interacting with a ligand-bound second receptor. ALK activation can be abolished through PXL mutation or with PXL-targeting antibodies. Together, these results explain how ALK uses its atypical architecture for its regulation, and suggest new therapeutic opportunities for ALK-expressing cancers such as paediatric neuroblastoma.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Structure of the ALK–ALKAL complex and the ALK GRD.
Fig. 2: Ligand binding is directed by the C-terminal loop of ALK.
Fig. 3: Dimerization of ALK is directed by the PXL.
Fig. 4: Antibodies to the C-terminal loop or PXL prevent ALK activation.

Data availability

The refined structural protein models and corresponding structure–factor amplitudes have been deposited under PDB accession codes 7LS0 (human ALK GRD–ALKAL fusion complex), 7LRZ (human ALK GRD), 7LIR (worm ALK GRD) and 7MK7 (ALKAL2-AD).


  1. 1.

    Weiss, J. B. et al. Anaplastic lymphoma kinase and leukocyte tyrosine kinase: functions and genetic interactions in learning, memory and adult neurogenesis. Pharmacol. Biochem. Behav. 100, 566–574 (2012).

    CAS  Article  Google Scholar 

  2. 2.

    Orthofer, M. et al. Identification of ALK in thinness. Cell 181, 1246–1262.e1222, (2020).

    CAS  Article  Google Scholar 

  3. 3.

    Hallberg, B. & Palmer, R. H. Mechanistic insight into ALK receptor tyrosine kinase in human cancer biology. Nat. Rev. Cancer 13, 685–700 (2013).

    CAS  Article  Google Scholar 

  4. 4.

    Carpenter, E. L. et al. Antibody targeting of anaplastic lymphoma kinase induces cytotoxicity of human neuroblastoma. Oncogene 31, 4859–4867 (2012).

    CAS  Article  Google Scholar 

  5. 5.

    Mosse, Y. P. et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature 455, 930–935 (2008).

    ADS  CAS  Article  Google Scholar 

  6. 6.

    Trigg, R. M. & Turner, S. D. ALK in neuroblastoma: biological and therapeutic implications. Cancers 10, 113 (2018).

    Article  Google Scholar 

  7. 7.

    Borenas, M. et al. ALK ligand ALKAL2 potentiates MYCN-driven neuroblastoma in the absence of ALK mutation. EMBO J. 40, e105784 (2021).

    Article  Google Scholar 

  8. 8.

    Reshetnyak, A. V. et al. Augmentor α and β (FAM150) are ligands of the receptor tyrosine kinases ALK and LTK: hierarchy and specificity of ligand–receptor interactions. Proc. Natl Acad. Sci. USA 112, 15862–15867 (2015).

    ADS  CAS  Article  Google Scholar 

  9. 9.

    Guan, J. et al. FAM150A and FAM150B are activating ligands for anaplastic lymphoma kinase. eLife 4, e09811 (2015).

    Article  Google Scholar 

  10. 10.

    Lemmon, M. A. & Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 141, 1117–1134 (2010).

    CAS  Article  Google Scholar 

  11. 11.

    Loren, C. E. et al. A crucial role for the Anaplastic lymphoma kinase receptor tyrosine kinase in gut development in Drosophila melanogaster. EMBO Rep. 4, 781–786 (2003).

    CAS  Article  Google Scholar 

  12. 12.

    Zhang, H. et al. Deorphanization of the human leukocyte tyrosine kinase (LTK) receptor by a signaling screen of the extracellular proteome. Proc. Natl Acad. Sci. USA 111, 15741–15745 (2014).

    ADS  CAS  Article  Google Scholar 

  13. 13.

    Reshetnyak, A. V. et al. Identification of a biologically active fragment of ALK and LTK-ligand 2 (augmentor-α). Proc. Natl Acad. Sci. USA 115, 8340–8345 (2018).

    CAS  Article  Google Scholar 

  14. 14.

    Qin, L. Y. et al. Discovery of 7-(3-(piperazin-1-yl)phenyl)pyrrolo[2,1-f][1,2,4]triazin-4-amine derivatives as highly potent and selective PI3Kδ inhibitors. Bioorg. Med. Chem. Lett. 27, 855–861 (2017).

    CAS  Article  Google Scholar 

  15. 15.

    Youn, S. J. et al. Construction of novel repeat proteins with rigid and predictable structures using a shared helix method. Sci. Rep. 7, 2595 (2017).

    ADS  Article  Google Scholar 

  16. 16.

    Holm, L. DALI and the persistence of protein shape. Protein Sci. 29, 128–140 (2020).

    CAS  Article  Google Scholar 

  17. 17.

    Eck, M. J. & Sprang, S. R. The structure of tumor necrosis factor-α at 2.6 Å resolution. Implications for receptor binding. J. Biol. Chem. 264, 17595–17605 (1989).

    CAS  Article  Google Scholar 

  18. 18.

    Warkentin, E. et al. A rare polyglycine type II-like helix motif in naturally occurring proteins. Proteins 85, 2017–2023 (2017).

    CAS  Article  Google Scholar 

  19. 19.

    Crick, F. H. & Rich, A. Structure of polyglycine II. Nature 176, 780–781 (1955).

    ADS  CAS  Article  Google Scholar 

  20. 20.

    Dunne, M. et al. Salmonella phage S16 tail fiber adhesin features a rare polyglycine rich domain for host recognition. Structure 26, 1573–1582.e1574 (2018).

    CAS  Article  Google Scholar 

  21. 21.

    Vadas, O., Jenkins, M. L., Dornan, G. L. & Burke, J. E. Using hydrogen–deuterium exchange mass spectrometry to examine protein–membrane interactions. Methods Enzymol. 583, 143–172 (2017).

    CAS  Article  Google Scholar 

  22. 22.

    Sano, R. et al. An antibody–drug conjugate directed to the ALK receptor demonstrates efficacy in preclinical models of neuroblastoma. Sci. Transl. Med. 11, eaau9732 (2019).

    Article  Google Scholar 

  23. 23.

    Tate, J. G. et al. COSMIC: the catalogue of somatic mutations in cancer. Nucleic Acids Res. 47, D941–D947 (2019).

    CAS  Article  Google Scholar 

  24. 24.

    Ishihara, T. et al. HEN-1, a secretory protein with an LDL receptor motif, regulates sensory integration and learning in Caenorhabditis elegans. Cell 109, 639–649 (2002).

    CAS  Article  Google Scholar 

  25. 25.

    Englund, C. et al. Jeb signals through the Alk receptor tyrosine kinase to drive visceral muscle fusion. Nature 425, 512–516 (2003).

    ADS  CAS  Article  Google Scholar 

  26. 26.

    Lee, H. H., Norris, A., Weiss, J. B. & Frasch, M. Jelly belly protein activates the receptor tyrosine kinase Alk to specify visceral muscle pioneers. Nature 425, 507–512 (2003).

    ADS  CAS  Article  Google Scholar 

  27. 27.

    Murray, P. B. et al. Heparin is an activating ligand of the orphan receptor tyrosine kinase ALK. Sci. Signal. 8, ra6 (2015).

    Article  Google Scholar 

  28. 28.

    Reshetnyak, A. V. et al. Mechanism for the activation of the anaplastic lymphoma kinase receptor. Nature (2021).

  29. 29.

    Jenni, S., Goyal, Y., von Grotthuss, M., Shvartsman, S. Y. & Klein, D. E. Structural basis of neurohormone perception by the receptor tyrosine kinase torso. Mol. Cell. 60, 941–952 (2015).

    CAS  Article  Google Scholar 

  30. 30.

    Klein, D. E., Stayrook, S. E., Shi, F., Narayan, K. & Lemmon, M. A. Structural basis for EGFR ligand sequestration by Argos. Nature 453, 1271–1275 (2008).

    ADS  CAS  Article  Google Scholar 

  31. 31.

    Vonrhein, C., Blanc, E., Roversi, P. & Bricogne, G. Automated structure solution with autoSHARP. Methods Mol. Biol. 364, 215–230 (2007).

    CAS  PubMed  Google Scholar 

  32. 32.

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

    Article  Google Scholar 

  33. 33.

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    CAS  Article  Google Scholar 

  34. 34.

    Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171–1179 (2008).

    CAS  Article  Google Scholar 

  35. 35.

    Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).

    CAS  Article  Google Scholar 

  36. 36.

    Morin, A. et al. Collaboration gets the most out of software. eLife 2, e01456 (2013).

    Article  Google Scholar 

  37. 37.

    Patil, K., et al Computational studies of anaplastic lymphoma kinase mutations reveal common mechanisms of oncogenic activation. Proc. Natl Acad. Sci. USA (in the press).

  38. 38.

    Grimm, J. B. et al. A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat. Methods 12, 244–250 (2015).

    CAS  Article  Google Scholar 

  39. 39.

    Kabsch, W. Xds. Acta Crystallogr. D 66, 125–132 (2010).

    CAS  Article  Google Scholar 

  40. 40.

    Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011).

    CAS  Article  Google Scholar 

  41. 41.

    Adams, P. D. et al. The Phenix software for automated determination of macromolecular structures. Methods 55, 94–106 (2011).

    CAS  Article  Google Scholar 

Download references


We thank C. Alarcon, Y. Liu, J. Abraham and their laboratories for valuable discussions, as well as members of the Klein, Lemmon and Schlessinger laboratories; A. Reshetnyak, D. Puleo and J. Mohanty for their contributions. This work was supported by the NIH, NIGMS grant R35 GM122485 (to M.A.L.), and NCI grant R01 CA248532 (to D.E.K.). This work is based in part on research conducted at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P30 GM124165). The Pilatus 6M detector on 24-ID-C beam line is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. GM/CA@APS has been funded in whole or in part with Federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The Eiger 16M detector at GM/CA-XSD was funded by NIH grant S10 OD012289.

Author information




D.E.K. designed the overall project, with input from M.A.L. and J.S. D.E.K. wrote the manuscript assisted by T.L., with input from all authors. T.L. generated all materials (assisted by J.Z., O.B. and I.X.W.) and performed all solution biophysical studies. T.L., S.E.S. and D.E.K. analysed ALK structures. T.L. performed cell assays (assisted by Y.W. and H.L.). T.L. and Y.T. carried out HDX-MS studies, supervised by M.A.L. T.L. and K.C.M. performed fluorescence studies in membranes, supervised by M.A.L. I.L. carried out full length ALK studies with help from M.A. and Y.S. ALKAL1 AD–MBP structural studies and analysis was performed by S.G.K., supervised by J.S. Purified CDX antibodies were provided by A.P. and D.A.

Corresponding author

Correspondence to Daryl E. Klein.

Ethics declarations

Competing interests

J.S. is a member of the scientific advisory board of Celldex. D.A. is an employee of Celldex Therapeutics.

Additional information

Peer review information Nature thanks the anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Structural comparison of human and invertebrate ALK.

a, Size exclusion chromatography of each protein was carried out using a Superdex 75 Increase 10/300 GL column. The non-glycosylated mass was calculated from the protein sequence. The mass corresponding to each SEC peak was determined based on the log (MW) versus elution volume plot of standards for the column. The SEC peak mass of each protein is consistent with a glycosylated monomer. b, ALK’s glycine helices project downward from the TNF-α like region. Unique to ALK, strand 10 crosses over strands 4 and 5 to terminate the fold, producing a surface terminal loop, “C-term loop”. The GRD has a distinct topology, and does not form the jelly-roll characteristic of TNF-α domains c, The GRD of human ALK. d, The hexagonal array of the Pole, and e, the order and topology of the Pole (red circles into the page, black out of the page). f, C. elegans ALK adopts a similar overall architecture to the human GRD. However, the invertebrate PXL is structurally different, forming a β-hairpin rather than helices (orange). g, The Pole of invertebrate ALK is also smaller, with 11 glycine helices that form 2 complete hexagons. h, The helical strands are in the same order and topology as in human ALK. Interestingly, the missing glycine helices of the invertebrate Pole are partially matched by non PG-II loops that interact with the hexagonal array (dashed circles). The invertebrate GRD structure additionally includes a C-terminal cysteine-rich region that leads up to the transmembrane domain. This region has 10 cysteines and forms 2 EGF-like domains (f, blue).

Extended Data Fig. 2 Structure of invertebrate ALK’s EGF-like domains.

a, The first EGF-like domain has canonical disulfide pairing. b, The second EGF-like domain is atypical in that it lacks the first 1-3 disulfide bond, the stabilizing role of which is replaced by hydrophobic interactions involving Y871 and F859. c, The EGF-like domains pack tightly to the TNF-α like domain with hydrophobic interactions. Y836 and F837 of the first EGF domain bind to the proximal C-terminal loop. F874 of the second EGF like domain is buried in a hydrophobic cavity.

Extended Data Fig. 3 HDX analysis of ALKAL binding to ALK.

HDX-MS percent exchange butterfly plot for ALKAL2-AD binding to human ALK GRD. Each peptide is assigned a peptide ID number (Extended Data Table 2) from the N- (left) to the C-terminus (right). Each grey bar shows the sum of ∆%Exchange at all labeling timepoints (∆%sum) for each peptide. The dotted purple line corresponds to statistically significant ∆%sum (16%, or ± 0.77 Da difference in deuterium uptake between unliganded and ALKAL-bound GRD) with 98 % confidence limit calculated based on the measured standard deviation of deuterium uptake for each peptide. Regions with positive or negative ∆%Exchange become more stable or flexible, respectively, upon ALKAL binding. Statistics were derived from two independent biological repeats, each with three technical repeats. Data represent mean ± SD.

Extended Data Fig. 4 ALK binding and signaling by ALKAL2-AD.

a, Representative BLI sensograms traces (black) and kinetic fittings (red). Fitting was carried out using ForteBio Data Analysis 10.0 software using 1:1 model with Rmax linked global fitting. Where appropriate, kinetic fit parameters are included. b, c, NIH 3T3 cells stably expressing wild type (WT) or mutated full length ALK, stimulated with high concentrations (10 nM) of ALKAL2 to assess residual signaling ability. b, Single point mutations of conserved binding-site residues. E978R has the greatest impact on ALKAL induced ALK signaling in agreement with binding data. c, C-terminal conserved glutamates mutated to the residues found at the same position in invertebrate ALK. The double (E974L/E978Y) mutant fails to signal, consistent with it being the only mutation shown here that completely abolished ligand binding in (a) (Extended Data Table 3). For gel source data, see Supplementary Fig. 2. The stimulation experiment was repeated three times with similar results.

Extended Data Fig. 5 Ligand binding and receptor dimerization are coupled to Pole rotation and PXL changes.

a, View looking down the long axis of the Pole with apo ALK (gray) aligned to the complex structure (color). Compared to unliganded ALK, the ligand-bound ALK dimer undergoes a clockwise rotation of the Pole about the central glycine helix (number 4). b, Unliganded ALK (gray) aligned to both protomers of the complex dimer (color). The PXL residues surrounding Q788 adopt a helical structure upon ligand binding and dimerization. c, Upon ligand binding, two additional peptides – not directly involved in ligand binding and discussed in Fig. 2 – are significantly protected. Statistics were derived from two independent biological repeats, each with three technical repeats. Data represent mean ± SD. d, these peptides (cyan) (peptide #1 and #21, Extended Data Fig. 3) correspond to the dimer interface including the disulfide linked helix of the PXL (#21) and the helix on the TNF-α like domain it forms a bond with (#1). e, The core helix-turn-helix of the AD is largely unaltered upon binding. ALKAL2 from the ALK-ALKAL fusion complex structure (green) is aligned to an un-complexed ALKAL1-AD MBP (Maltose Binding Protein) fusion (cyan).

Extended Data Fig. 6 The PXL region is necessary for ALK signaling.

a, Binding of ALKAL2-AD to GRD PXL mutations detected by BLI. The sensors were loaded with ALKAL2-AD. REQ is a mutant that alters the interface residues 795-“IGE”-797 (shown in Fig. 3b, c) to REQ. ΔPXL is a mutant that removes the entire “disulfided helix” 783-797 (shown in Fig. 3b, c). The relative binding is the binding normalized to the maximum responses. Data represent mean ± SD of four measurements. b, Expression of Halo-ALK on NIH/3T3 cell membranes. NIH/3T3 cells were untransfected, transfected with wildtype Halo-ALK or ALK mutants. Cells were stained with membrane impermeable dye, JF549i, before imaging. For each construct fluorescence (top row), brightfield (middle row), and a merge (bottom row) were shown. Scale bar 5 µm. The experiment was repeated two times with similar results. c, Binding of CDX123 or CDX125 to GRD or GRDΔPXL detected by BLI. Data represent mean ± SD from three independent experiments.

Extended Data Fig. 7 Implications for GRD mutation and evolution.

a, Invertebrate ALK GRD structure with known glycine-to-acidic residue (D/E) mutations highlighted (purple spheres)9. b, Human ALK GRD structure with all of glycine-to-acidic residue mutations found in the COSMIC database ( highlighted (purple spheres). c, Invertebrate ALK GRD does not bind to human ALKAL2-AD. The relative binding is the binding normalized to the maximum responses. Data represent mean ± SD of three measurements. d, The EGF-like domain of invertebrate ALK occupies a region of the C-terminal loop required for ALKAL binding. This would prevent binding of any similar helix-loop-helix like ligand.

Extended Data Table 1 Data collection and refinement statistics
Extended Data Table 2 HDX peptides
Extended Data Table 3 Binding analysis of GRD and ALKAL mutants

Supplementary information

Supplementary Information

See Supplementary Information for contents

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Li, T., Stayrook, S.E., Tsutsui, Y. et al. Structural basis for ligand reception by anaplastic lymphoma kinase. Nature (2021).

Download citation

Further reading


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.


Quick links