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Cryo-EM structures of Toll-like receptors in complex with UNC93B1

Nature Structural & Molecular Biology volume 28, pages 173–180 (2021)Cite this article

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Abstract

Nucleic acid–sensing Toll-like receptors (TLRs) play a pivotal role in innate immunity by recognizing foreign DNA and RNA. Compartmentalization of these TLRs in the endosome limits their activation by self-derived nucleic acids and reduces the possibility of autoimmune reactions. Although chaperone Unc-93 homolog B1, TLR signaling regulator (UNC93B1) is indispensable for the trafficking of TLRs from the endoplasmic reticulum to the endosome, mechanisms of UNC93B1-mediated TLR regulation remain largely unknown. Here, we report two cryo-EM structures of human and mouse TLR3–UNC93B1 complexes and a human TLR7–UNC93B1 complex. UNC93B1 exhibits structural similarity to the major facilitator superfamily transporters. Both TLRs interact with the UNC93B1 amino-terminal six-helix bundle through their transmembrane and luminal juxtamembrane regions, but the complexes of TLR3 and TLR7 with UNC93B1 differ in their oligomerization state. The structural information provided here should aid in designing compounds to combat autoimmune diseases.

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Fig. 1: Structure of UNC93B1 in complex with TLR3.
Fig. 2: Detailed views of UNC93B1 recognition by TLR3.
Fig. 3: Structure of UNC93B1 in complex with TLR7.
Fig. 4: UNC93B1 inhibits the formation of the activated TLR dimer.

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Data availability

Cryo-EM maps are deposited in the Electron Microscopy Data Bank under accession codes EMD-30293 (human TLR3–UNC93B1), EMD-30294 (mouse TLR3–UNC93B1) and EMD-30501 (human TLR7–UNC93B1). Structure coordinates are deposited in the wwPDB under accession codes PDB 7C76 (human TLR3–UNC93B1), PDB 7C77 (mouse TLR3–UNC93B1) and PDB 7CYN (human TLR7–UNC93B1). Source data are provided with this paper.

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Acknowledgements

We thank A. Tsutsumi, Y. Sakamaki, M. Kikkawa (Cryo-EM facility in the University of Tokyo) and M. Yamamoto (RIKEN RSC Cryo-EM facility) for their help in cryo-EM data collection. We thank R. Fukui and K. Miyake for their helpful discussion on this manuscript. This work was supported by a Grant-in-Aid from the Japanese Ministry of Education, Culture, Sports, Science, and Technology grant nos. 20K16274 (H.I.), 26711002 (U.O.) and 19H00976 (T.S.); CREST, JST (T.S.); the Takeda Science Foundation (U.O. and T.S.); the Mochida Memorial Foundation for Medical and Pharmaceutical Research (U.O.); the Daiichi Sankyo Foundation of Life Science (U.O.); the Uehara Memorial Foundation (U.O. and T.S.); and the Naito Foundation (U.O. and T.S.). This work is partially supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from Japan Agency for Medical Research and Development (AMED) under grant number JP19am0101115, JP19am0101070 (to H.S.). This work was supported in part by the RIKEN Dynamic Structural Biology project (to H.S.).

Author information

Authors and Affiliations

  1. Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan

    Hanako Ishida, Jinta Asami, Zhikuan Zhang, Umeharu Ohto & Toshiyuki Shimizu

  2. Graduate School of Science, The University of Tokyo, Tokyo, Japan

    Tomohiro Nishizawa

  3. RIKEN SPring-8 Center, Hyogo, Japan

    Hideki Shigematsu

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Contributions

H.I. and U.O. designed the experiments. H.I. prepared recombinant proteins. H.I. and J.A. performed pull-down experiments. H.I. and U.O. performed cryo-EM analyses with assistance from Z.Z., T.N. and H.S. H.I., U.O. and T.S. wrote the paper with assistance from all the authors. U.O. and T.S. supervised the project.

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Correspondence to Umeharu Ohto or Toshiyuki Shimizu.

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The authors declare no competing interests.

Additional information

Peer review information Nature Structural & Molecular Biology thanks Gregory Barton, Bostjan Kobe and Eicke Latz for their contribution to the peer review of this work. Anke Sparmann was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Sample preparation and cryo-EM analysis of human TLR3-UNC93B1 complex.

a Representative size-exclusion chromatography profile of human TLR3-UNC93B1 complex (left) and SDS-PAGE analysis of the purified sample stained with Coomassie blue (right). Pooled fractions are shown with the bar. Absorbances at 280 nm and 260 nm are shown with solid and dashed lines, respectively. An uncropped image is available as Supplementary Data. b Data processing workflow of cryo-EM analysis of human TLR3-UNC93B1 complex. Representative motion-corrected micrograph, 2D class averages, and 3D class-averages, gold-standard FSC curve of the final 3D reconstruction (resolution cutoff at FSC = 0.143), and the final 3D-map colored according to the local resolution are shown. The 2D class averages were calculated using the refined particles that was used for the final reconstruction. The 3D classes selected for following analysis are indicated with red boxes.

Extended Data Fig. 2 Sample preparation and cryo-EM analysis of mouse TLR3-UNC93B1 complex.

a Representative size-exclusion chromatography profile of mouse TLR3-UNC93B1 complex (left) and SDS-PAGE analysis of the purified sample stained with Coomassie blue (right). Pooled fractions are shown with the bar. Absorbances at 280 nm and 260 nm are shown with solid and dashed lines, respectively. An uncropped image is available as Supplementary Data. b Data processing workflow of cryo-EM analysis of mouse TLR3-UNC93B1 complex. Representative motion-corrected micrograph, 3D class-averages, Gold-standard FSC curve of the final 3D reconstruction (resolution cutoff at FSC = 0.143), and the final 3D-map colored according to the local resolution are shown. The 3D classes selected for following analysis are indicated with red boxes.

Extended Data Fig. 3 Cryo-EM density maps.

a Cryo-EM density maps of human TLR3-UNC93B1 complex around each TM helix of TLR3 and UNC93B1 are shown. b Cryo-EM density map for N-glycans of human TLR3-UNC93B1 complex. The Asn residues to which N-glycans were attached are labeled. c Cryo-EM density map for N-glycans of human TLR7-UNC93B1 complex. The Asn residues to which N-glycans were attached are labeled.

Extended Data Fig. 4 Structural comparisons of TLR3-UNC93B1 complex.

a Structural superposition of human and mouse TLR3-UNC93B1 complexes and sequence alignment of TLR3 from various species. The Cys residues forming conserved disulfide bonds in LRR-CT are highlighted with yellow. b Structural comparison between the cryo-EM structure of UNC93B1-bound TLR3 and the crystal structures of unliganded human TLR320 (PDB 1ZIW) and dsRNA-bound mouse TLR319 (PDB 3CIY). The UNC93B1 molecule in the TLR3-UNC93B1 complex, and the dsRNA and the other protomer of TLR3 in the dsRNA-bound TLR3 are shown in semitransparent representation.

Extended Data Fig. 5 Structural similarity with major facilitator superfamily transporters.

Structural similarity of UNC93B1 with major facilitator superfamily transporters. The UNC93B1 from human TLR3-UNC93B1 complex (this study), lipoteichoic acids flippase23 (PDB 6S7V), fucose/H+ symporter24 (PDB 3O7Q), and phosphate transporter25 (PDB 4J05). The N- and C-termini are indicated. The structures are colored from blue to red from the N to C terminus.

Extended Data Fig. 6 Sample preparation and cryo-EM analysis of human TLR7-UNC93B1 complex.

a Representative size-exclusion chromatography profile of human TLR7-UNC93B1 complex (left) and SDS-PAGE analysis of the purified sample stained with Coomassie blue (right). Pooled fractions are shown with the bar. Absorbances at 280 nm and 260 nm are shown with solid and dashed lines, respectively. Uncropped images are available as Supplementary Data. b Data processing workflow of cryo-EM analysis of human TLR7-UNC93B1 complex. Representative motion-corrected micrograph, 2D class averages, and 3D class-averages, Gold-standard FSC curve of the final 3D reconstruction (resolution cutoff at FSC = 0.143), and the final 3D-map colored according to the local resolution are shown. The 2D class averages were calculated using the refined particles that was used for the final reconstruction. The 3D classes selected for following analysis are indicated with red boxes.

Extended Data Fig. 7 Comparison of LRR-CT, juxtamembrane, and TM regions from different members of TLRs.

a Sequence alignment of LRR-CT, juxtamembrane, and TM regions from different members of TLRs. The conserved Phe and His residues among TLR3, TLR7, TLR8, TLR9 in the TM regions are indicated by red boxes. b Structural comparison of the LRR-CT, juxtamembrane, and TM regions of TLR3 from TLR3-UNC93B1 complex (this study, left), TLR7 from TLR7-UNC93B1 complex (this study, right). The two conserved disulfide bonds in LRR-CT are shown with sticks. c Electrostatic surface potential of the TLR7-UNC93B1 complex. Positive and negative electrostatic potentials are shown in blue and red, respectively.

Extended Data Fig. 8 Comparison of dimer structures of TLR7-UNC93B1 complex and unliganded TLR8.

a Structure of human TLR7-UNC93B1 complex (this study). The disordered C-terminal linker (dashed line) and TIR domain40 (PDB 1FYV) is modeled. b Structure of unliganded human TLR827 (PDB 3W3G). Each protomer in the dimer is shown in different colors.

Extended Data Fig. 9 Mutations of UNC93B1 on the structure.

The reported mutations9,10,12,13,14,15,18,28 that affect UNC93B1 function are mapped onto the structure of human TLR3-UNC93B1 complex. The side chains of these residues are shown with sticks and labeled.

Supplementary information

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Supplementary Fig. 1.

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Supplementary Data

Unprocessed gel image for Figs. 1b and 2f and Extended Data Figs. 1a, 2a and 6a.

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Ishida, H., Asami, J., Zhang, Z. et al. Cryo-EM structures of Toll-like receptors in complex with UNC93B1. Nat Struct Mol Biol 28, 173–180 (2021). https://doi.org/10.1038/s41594-020-00542-w

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