The cryo-electron microscopy structure of huntingtin


Huntingtin (HTT) is a large (348 kDa) protein that is essential for embryonic development and is involved in diverse cellular activities such as vesicular transport, endocytosis, autophagy and the regulation of transcription1,2. Although an integrative understanding of the biological functions of HTT is lacking, the large number of identified HTT interactors suggests that it serves as a protein–protein interaction hub1,3,4. Furthermore, Huntington’s disease is caused by a mutation in the HTT gene, resulting in a pathogenic expansion of a polyglutamine repeat at the amino terminus of HTT5,6. However, only limited structural information regarding HTT is currently available. Here we use cryo-electron microscopy to determine the structure of full-length human HTT in a complex with HTT-associated protein 40 (HAP40; encoded by three F8A genes in humans)7 to an overall resolution of 4 Å. HTT is largely α-helical and consists of three major domains. The amino- and carboxy-terminal domains contain multiple HEAT (huntingtin, elongation factor 3, protein phosphatase 2A and lipid kinase TOR) repeats arranged in a solenoid fashion. These domains are connected by a smaller bridge domain containing different types of tandem repeats. HAP40 is also largely α-helical and has a tetratricopeptide repeat-like organization. HAP40 binds in a cleft and contacts the three HTT domains by hydrophobic and electrostatic interactions, thereby stabilizing the conformation of HTT. These data rationalize previous biochemical results and pave the way for improved understanding of the diverse cellular functions of HTT.

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Figure 1: Purification of the HTT–HAP40 complex.
Figure 2: Architecture of the HTT–HAP40 complex.
Figure 3: Structure of HTT domains.
Figure 4: Structural basis of the HTT–HAP40 interaction.

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  1. 1

    Saudou, F. & Humbert, S. The biology of huntingtin. Neuron 89, 910–926 (2016)

    CAS  Article  Google Scholar 

  2. 2

    Zuccato, C. & Cattaneo, E. in Huntington’s Disease 4th edn (eds Bates, G. et al.) Ch. 11 (Oxford Univ. Press, 2014)

  3. 3

    Kaltenbach, L. S. et al. Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS Genet. 3, e82 (2007)

    Article  Google Scholar 

  4. 4

    Shirasaki, D. I. et al. Network organization of the huntingtin proteomic interactome in mammalian brain. Neuron 75, 41–57 (2012)

    CAS  Article  Google Scholar 

  5. 5

    MacDonald, M. E. et al. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington’s disease chromosomes. Cell 72, 971–983 (1993)

    Article  Google Scholar 

  6. 6

    Finkbeiner, S. Huntington’s disease. Cold Spring Harb. Perspect. Biol. 3, a007476 (2011)

    Article  Google Scholar 

  7. 7

    Peters, M. F. & Ross, C. A. Isolation of a 40-kDa Huntingtin-associated protein. J. Biol. Chem. 276, 3188–3194 (2001)

    CAS  Article  Google Scholar 

  8. 8

    Palidwor, G. A. et al. Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PLoS Comput. Biol. 5, e1000304 (2009)

    Article  Google Scholar 

  9. 9

    Vijayvargia, R. et al. Huntingtin’s spherical solenoid structure enables polyglutamine tract-dependent modulation of its structure and function. eLife 5, e11184 (2016)

    Article  Google Scholar 

  10. 10

    Andrade, M. A. & Bork, P. HEAT repeats in the Huntington’s disease protein. Nat. Genet. 11, 115–116 (1995)

    CAS  Article  Google Scholar 

  11. 11

    Takano, H. & Gusella, J. F. The predominantly HEAT-like motif structure of huntingtin and its association and coincident nuclear entry with dorsal, an NF-kB/Rel/dorsal family transcription factor. BMC Neurosci. 3, 15 (2002)

    Article  Google Scholar 

  12. 12

    Tartari, M. et al. Phylogenetic comparison of huntingtin homologues reveals the appearance of a primitive polyQ in sea urchin. Mol. Biol. Evol. 25, 330–338 (2008)

    CAS  Article  Google Scholar 

  13. 13

    Seong, I. S. et al. Huntingtin facilitates polycomb repressive complex 2. Hum. Mol. Genet. 19, 573–583 (2010)

    CAS  Article  Google Scholar 

  14. 14

    Wetzel, R. & Mishra, R. in Huntington’s Disease 4th edn (eds Bates, G. et al.) Ch. 12 (Oxford Univ. Press, 2014)

  15. 15

    Li, W., Serpell, L. C., Carter, W. J., Rubinsztein, D. C. & Huntington, J. A. Expression and characterization of full-length human huntingtin, an elongated HEAT repeat protein. J. Biol. Chem. 281, 15916–15922 (2006)

    CAS  Article  Google Scholar 

  16. 16

    Pal, A., Severin, F., Lommer, B., Shevchenko, A. & Zerial, M. Huntingtin–HAP40 complex is a novel Rab5 effector that regulates early endosome motility and is up-regulated in Huntington’s disease. J. Cell Biol. 172, 605–618 (2006)

    CAS  Article  Google Scholar 

  17. 17

    Huang, B. et al. Scalable production in human cells and biochemical characterization of full-length normal and mutant huntingtin. PLoS ONE 10, e0121055 (2015)

    Article  Google Scholar 

  18. 18

    Chari, A. et al. ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space. Nat. Methods 12, 859–865 (2015)

    CAS  Article  Google Scholar 

  19. 19

    Buchan, D. W., Minneci, F., Nugent, T. C., Bryson, K. & Jones, D. T. Scalable web services for the PSIPRED protein analysis workbench. Nucleic Acids Res. 41, W349–W357 (2013)

    Article  Google Scholar 

  20. 20

    Arndt, J. R., Chaibva, M. & Legleiter, J. The emerging role of the first 17 amino acids of huntingtin in Huntington’s disease. Biomol. Concepts 6, 33–46 (2015)

    CAS  Article  Google Scholar 

  21. 21

    Yanai, A. et al. Palmitoylation of huntingtin by HIP14 is essential for its trafficking and function. Nat. Neurosci. 9, 824–831 (2006)

    CAS  Article  Google Scholar 

  22. 22

    Kegel, K. B. et al. Huntingtin associates with acidic phospholipids at the plasma membrane. J. Biol. Chem. 280, 36464–36473 (2005)

    CAS  Article  Google Scholar 

  23. 23

    Wellington, C. L. et al. Caspase cleavage of gene products associated with triplet expansion disorders generates truncated fragments containing the polyglutamine tract. J. Biol. Chem. 273, 9158–9167 (1998)

    CAS  Article  Google Scholar 

  24. 24

    El-Daher, M. T. et al. Huntingtin proteolysis releases non-polyQ fragments that cause toxicity through dynamin 1 dysregulation. EMBO J. 34, 2255–2271 (2015)

    CAS  Article  Google Scholar 

  25. 25

    Luo, S., Vacher, C., Davies, J. E. & Rubinsztein, D. C. Cdk5 phosphorylation of huntingtin reduces its cleavage by caspases: implications for mutant huntingtin toxicity. J. Cell Biol. 169, 647–656 (2005)

    CAS  Article  Google Scholar 

  26. 26

    Schilling, B. et al. Huntingtin phosphorylation sites mapped by mass spectrometry. Modulation of cleavage and toxicity. J. Biol. Chem. 281, 23686–23697 (2006)

    CAS  Article  Google Scholar 

  27. 27

    Ratovitski, T. et al. Post-translational modifications (PTMs), identified on endogenous huntingtin, cluster within proteolytic domains between HEAT repeats. J. Proteome Res. 16, 2692–2708 (2017)

    CAS  Article  Google Scholar 

  28. 28

    Ratovitski, T. et al. Mutant huntingtin N-terminal fragments of specific size mediate aggregation and toxicity in neuronal cells. J. Biol. Chem. 284, 10855–10867 (2009)

    CAS  Article  Google Scholar 

  29. 29

    Gusella, J. F. & MacDonald, M. E. Huntingtin: a single bait hooks many species. Curr. Opin. Neurobiol. 8, 425–430 (1998)

    CAS  Article  Google Scholar 

  30. 30

    Vedadi, M. et al. Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc. Natl Acad. Sci. USA 103, 15835–15840 (2006)

    CAS  ADS  Article  Google Scholar 

  31. 31

    Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005)

    Article  Google Scholar 

  32. 32

    Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017)

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012)

    CAS  Article  Google Scholar 

  34. 34

    Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015)

    Article  Google Scholar 

  35. 35

    Moriya, T. et al. High-resolution single particle analysis from electron cryo-microscopy images using SPHIRE. J. Vis. Exp. 123, e55448 (2017)

    Google Scholar 

  36. 36

    Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012)

    CAS  Article  Google Scholar 

  37. 37

    Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)

    CAS  Article  Google Scholar 

  38. 38

    The PyMOL Molecular Graphics System v.1.8 (Schrödinger, 2015)

  39. 39

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

    Article  Google Scholar 

  40. 40

    Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    CAS  Article  Google Scholar 

  41. 41

    Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)

    CAS  PubMed  PubMed Central  Google Scholar 

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We thank J. Plitzko for electron microscopy support, F. Beck for help with image processing, E. Conti, H. Kiefer, B. Landwehrmeyer, K. Lindenberg, P. Mittl and L. Toledo-Sherman for discussions and A. Bracher, M. Hipp and E. Sakata for the critical reading of the manuscript. This work has been funded by the CHDI Foundation, the German Federal Ministry of Education and Research (FTLDc 01GI1007A), the German Research Foundation (SFB1279) and the European Commission (grant FP7 GA ERC-2012-SyG_318987–ToPAG). Q.G. is the recipient of postdoctoral fellowships from EMBO (EMBO ALTF 73-2015) and the Alexander von Humboldt Foundation.

Author information




Q.G., B.H., P.O., A.P., W.B., R.F.-B. and S.K. designed experiments. F.M., M.M. and A.P. performed differential scanning fluorimetry studies. P.O. performed mass spectrometry analyses. B.H. prepared the HTT–HAP40 samples for cryo-EM and performed the majority of the biochemical work together with T.E. M.S. performed the experiments with truncated HAP40 constructs. Q.G. performed the majority of the cryo-EM work. Q.G. and G.P. optimized sample conditions for cryo-EM. J.C. built the atomic model. Q.G., J.C. and R.F.-B. analysed the structure. Q.G., B.H., J.C., M.S., P.O., M.O., A.P., R.F.-B. and S.K. analysed the data. Q.G. and B.H. prepared the figures. Q.G., B.H., W.B., R.F.-B. and S.K. wrote the manuscript. All authors commented on the manuscript.

Corresponding authors

Correspondence to Wolfgang Baumeister or Rubén Fernández-Busnadiego or Stefan Kochanek.

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The authors declare no competing financial interests.

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Reviewer Information Nature thanks S. Scheres and R. Wetzel for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Figure 1 Sedimentation analysis by rate-zonal ultracentrifugation.

a, Flag-tag purified HTT (top) and Strep-tag purified HTT–HAP40 complex (bottom) analysed by rate-zonal ultracentrifugation followed by SDS–PAGE and Coomassie staining. Twenty-five fractions from 5–20% sucrose gradients were collected from the bottom of the tube; fractions 1–18 are shown here. Whereas HTT alone was present in fractions 1–18, the HTT–HAP40 complex was found mainly in fractions 15–17, indicating lower conformational heterogeneity. b, Western blot analysis of fractions 10–18 of the HTT–HAP40 complex. Coomassie stainings and western blots are representative of three independent experiments with similar results. For gel source images, see Supplementary Fig. 1.

Extended Data Figure 2 Cryo-EM analysis of the HTT–HAP40 complex.

a, Representative micrograph of HTT–HAP40 complex. b, 2D class averages. c, FSC plots. Cyan, gold-standard FSC curve; orange, FSC curve calculated between the cryo-EM map and the refined atomic model. FSC cut-off values of 0.143 and 0.5 were used for the half versus half and model versus map comparisons, respectively. The initial and final numbers of micrographs and particles were 707 and 635 and 418,627 and 98,310, respectively. d, Final density map of the HTT–HAP40 complex, coloured according to local resolution. The map was low-pass filtered to 4 Å and sharpened with a B-factor of −174 Å2. e, Detail of the electron density maps (mesh) for parts of HTT (top) and HAP40 (bottom). Source Data for the FSC plots are available online. Source data

Extended Data Figure 3 Atomic model of HTT within the HTT–HAP40 complex.

ad, The atomic model is shown in ribbon representation with a rainbow colour code from the N terminus (blue arrowhead in d) to the C terminus (red arrowhead in a). ad show different views of the complex, as indicated. Dashed lines mark unresolved regions.

Extended Data Figure 4 Amino acid sequences of 17QHTT and HAP40.

Structural elements of the atomic models are indicated as follows: elements not visible in the model (red boxes), unstructured regions (no box) and α-helices (yellow boxes). The sites of previously reported protease cleavage and post-translational modifications of HTT1,21,23,27 are indicated by text colour as follows: acetylation (dark blue), palmitoylation (red), phosphorylation (green) and proteolytic cleavage (cyan).

Extended Data Figure 5 PSIPRED secondary-structure predictions for HTT and HAP40.

Structural elements are indicated as follows: unstructured regions (no box), α-helices (yellow boxes) and β-sheet (grey box).

Extended Data Figure 6 Truncation analysis of HAP40 binding to HTT.

a, Schematic representation of the HAP40 constructs used in this study (all have C-terminal Strep-tags). b, HAP40 constructs were co-expressed with 17QHTT (bearing a C-terminal Flag-tag), immunoprecipitated using Strep-Tactin beads and analysed by western blot. Lanes are labelled as follows: 1, cell lysates; 2, cell lysates after incubation with Strep beads; 3, Strep-bead eluates. Note that full-length HAP40 and the construct lacking the central domain immunoprecipitate HTT, but constructs with deletion of the N- or C-terminal regions of HAP40 do not. Western blots are representative of two independent experiments with similar results. For gel source images, see Supplementary Fig. 1.

Extended Data Figure 7 Evolutionary analysis of HTT.

The human HTT model is shown in ribbon representation, coloured on the basis of sequence conservation across 16 metazoan species (Homo sapiens, Rattus norvegicus, Mus musculus, Sus scrofa, Bos taurus, Canis lupus familiaris, Monodelphis domestica, Gallus gallus, Danio rerio, Tetraodon nigroviridis, Fugu rubripes, Ciona savignyi, Ciona intestinalis, Strongylocentrotus purpuratus, Tribolium castaneum, Apis mellifera), using a previously reported sequence alignment12. The orientations of the HTT–HAP40 complex with respect to Fig. 2 are also indicated.

Extended Data Figure 8 Workflow for initial model validation for 3D reconstruction of the HTT–HAP40 complex.

A subset of particles with well-resolved 2D averages were used for initial model generation using RELION33 or SPHIRE35. The resulting models were used as reference for 3D classification of all the good particles. A featureless sphere was also used as a classification reference. Most of the particles were classified to identical structures with sufficient detail, indicating no reference bias in the reconstruction.

Extended Data Table 1 Cryo-EM data collection, refinement and validation statistics

Supplementary information

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Supplementary Figure 1

This file contains the uncropped scans with size marker indications. (PDF 419 kb)

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Guo, Q., Bin Huang, Cheng, J. et al. The cryo-electron microscopy structure of huntingtin. Nature 555, 117–120 (2018).

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