addenda and errata\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983

Targeting the innate immune receptor TLR8 using small-molecule agents. Corrigendum

aGraduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
*Correspondence e-mail: shimizu@mol.f.u-tokyo.ac.jp

(Received 6 August 2020; accepted 6 August 2020; online 25 August 2020)

Three of the figures in the article by Sakaniwa & Shimizu [(2020), Acta Cryst. D76, 621–629] were incorrectly annotated. Corrected figures are published here.

In the article by Sakaniwa & Shimizu (2020[Sakaniwa, K. & Shimizu, T. (2020). Acta Cryst. D76, 621-629.]) some residue labels were interchanged and hydrogen bonds were wrongly connected in Figs. 2, 3 and 5. In Fig. 2(g) the labels for D545* and D543* were interchanged and hydrogen bonds were wrongly connected. In Figs. 3(a)–3(c) the labels for D545* and D543* were interchanged and hydrogen bonds were wrongly connected. In Fig. 5(b) hydrogen bonds were wrongly connected.

Corrected figures are published here, and the main-chain atoms that were not involved in the interaction have been removed for clarity in Figs. 2(g)–2(i)[link], Fig. 3[link] and Fig. 5[link].

[Figure 2]
Figure 2
Structures of agonist-bound, unliganded and antagonist-bound forms. (a, b, c) The crystal structures of (a) agonist (R848)-bound, (b) unliganded and (c) antagonist (CU-CPT8m)-bound forms. A representative image of one protomer is colored blue and the other is colored orange and marked with an asterisk (*). The ligands are represented as ball-and-stick models in which C atoms are represented in yellow, O atoms in red and N atoms in blue. (d, e, f) The overall structures of (d) agonist-bound, (e) unliganded and (f) antagonist-bound forms. The leucine-rich repeat (LRRs) around the ligand-recognition sites are highlighted in purple (LRR8), cyan (LRR11–13), green (LRR15*–16*) and red (LRR17*–18*). The unoccupied pocket is shown by a white dashed rectangle. In the agonist-bound structure, the C-terminal regions are closer than those in the inactivated structures. The antagonist-bound structure was similar to the unliganded structure. (g, h, i) Close-up views around (g) the agonist-bound site (PDB entry 3w3l), (h) the unoccupied pocket (PDB entry 3w3g) and (i) the antagonist-bound site (PDB entry 5wyx). The chemical structure of each ligand is shown below the close-up view. Interactions of the agonist involve hydrophobic residues such as Phe346, Tyr348, Gly376, Val378, Ile403–Phe405, Val520*, Asp543*, Gly572*–Thr574* and some hydrogen bonds. Interactions of the antagonist involve hydrophobic residues such as Phe261, Phe346, Val378, Ile403, Phe405, Phe494*, Ala518*, Val520* and Tyr567*, stacking interactions with Tyr348 and Phe495* and some hydrogen bonds. LRR11–13 confront LRR15*–16* in the unliganded structure and the antagonist-bound structure, while LRR11–13 mainly interact with LRR17*–18* in the agonist-bound structure.
[Figure 3]
Figure 3
Close-up views of agonist recognition. (a, b, c) Close-up views around the agonist-bound site with (a) DS-877 (PDB entry 3wn4), (b) MB-564 (PDB entry 5awc) and (c) MB-343 (PDB entry 5az5). The agonists are represented as ball-and-stick models in which C atoms are represented in yellow, O atoms in red and N atoms in blue. Hydrogen bonds are indicated using dashed lines. The chemical structure of each ligand is shown below the close-up view.
[Figure 5]
Figure 5
Close-up views of antagonist recognition. (a, b, c) Close-up views around the antagonist-bound site with (a) CU-CPT9a (PDB entry 5z14), (b) CU-CPT9b (PDB entry 5wyz) and (c) CU-CPT9c (PDB entry 5z15). The agonists are represented as ball-and-stick models in which C atoms are represented in yellow, O atoms in red, N atoms in blue and chloride ions in green. Hydrogen bonds are shown as black dashed lines and the halogen bond is shown as a magenta dashed line. The chemical structure of each ligand is shown below the close-up view.

References

First citationSakaniwa, K. & Shimizu, T. (2020). Acta Cryst. D76, 621–629.  CrossRef IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
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