Nat Commun. 2018 Mar 22;9(1):1192. doi: 10.1038/s41467-018-03606-0.

Cryo-EM structure of the polycystic kidney disease-like channel PKD2L1.

Su Q^1,^2,³, Hu F^1,^3,⁴, Liu Y^4,^5,^6,⁷, Ge X^1,², Mei C⁸, Yu S⁸, Shen A⁸, Zhou Q^1,^3,^4,⁹, Yan C^1,^2,^3,⁹, Lei J^1,^2,³, Zhang Y^10,^11,^12,¹³, Liu X^14,^15,^16,^17,¹⁸, Wang T^19,^20,^21,²².

Author information

1: Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China.
2: School of Life Sciences, Tsinghua University, Beijing, 100084, China.
3: Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
4: School of Medicine, Tsinghua University, Beijing, 100084, China.
5: X-Lab for Transmembrane Signaling Research, Department of Biomedical Engineering and McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China.
6: School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
7: Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China, 102402.
8: Department of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200433, China.
9: Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
10: Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.
11: School of Life Sciences, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.
12: Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.
13: Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.
14: School of Life Sciences, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.
15: School of Medicine, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.
16: X-Lab for Transmembrane Signaling Research, Department of Biomedical Engineering and McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.
17: School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China. liu-lab@vip.163.com.
18: Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China, 102402. liu-lab@vip.163.com.
19: Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.
20: Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.
21: School of Medicine, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.
22: Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.

Abstract

PKD2L1, also termed TRPP3 from the TRPP subfamily (polycystic TRP channels), is involved in the sour sensation and other pH-dependent processes. PKD2L1 is believed to be a nonselective cation channel that can be regulated by voltage, protons, and calcium. Despite its considerable importance, the molecular mechanisms underlying PKD2L1 regulations are largely unknown. Here, we determine the PKD2L1 atomic structure at 3.38 Å resolution by cryo-electron microscopy, whereby side chains of nearly all residues are assigned. Unlike its ortholog PKD2, the pore helix (PH) and transmembrane segment 6 (S6) of PKD2L1, which are involved in upper and lower-gate opening, adopt an open conformation. Structural comparisons of PKD2L1 with a PKD2-based homologous model indicate that the pore domain dilation is coupled to conformational changes of voltage-sensing domains (VSDs) via a series of π-π interactions, suggesting a potential PKD2L1 gating mechanism.

PMID:: 29567962
PMCID:: PMC5864754
DOI:: 10.1038/s41467-018-03606-0

Free PMC Article

Images from this publication.See all images (6)Free text

Fig. 1

Structural characterizations of PKD2L1. a General topology of PKD2L1. PKD2 has a similar topology with a longer N-terminus and no oligomerization domain (OD). b Overall EM map of PKD2L1 (residues 64–629) colored according to different protomers. A swap structure feature can be visualized. Shown from the side view. c, d Overall structure of PKD2L1 (residues 64–629), view from the side and top, respectively. The structure is domain-colored as in panel a. The same color scheme was applied throughout the structural analysis in Figs. 1–, Supplementary Figs. and , and Supplementary Movies –. Glycosyl moieties are shown as sticks. All the above structure figures were prepared using PyMol (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.) and the EM map was generated using UCSF Chimera. e, f Ca²⁺ response I_Ca was elicited when [Ca²⁺]_o rapidly switched from 0 to 100 mM (green bar). Exemplar traces (e) for PKD2L1_WT (left) or PKD2L1_64–629 (right), both in complex with PKD1L3. Statistical summaries of I_Ca (f) for the peak amplitude, and the time constant of the decay phase (T_d). Number of cells for each group are indicated in the parentheses. PKD2L1_64–629 represents the truncated version of PKD2L1: 64–629, from which the Cryo-EM structure was resolved. g, h Acid response (I_pH) was induced when the stimulus of pH 2.5 (red bar) was quickly withdrawn. In all, 2 mM [Ca²⁺]_o was included in the bath solution for I_pH throughout this study. Exemplar traces (g) for PKD2L1_WT (left) or PKD2L1_64–629 (right), both in complex with PKD1L3. Statistical summaries of I_pH (h) for the peak amplitude, and the time constant of the decay phase (T_d). Intracellular buffer of 0.5 mM EGTA was used throughout. All above values are in mean ± SEM, indicated with significance (*p < 0.05; **p < 0.01; and ***p < 0.001). More detailed studies including the negative control can be found in our previous paper

Cryo-EM structure of the polycystic kidney disease-like channel PKD2L1

Nat Commun. 2018;9:1192.

Fig. 2

PKD2L1 pore suggests its open conformation in comparison with PKD2 structure. Throughout the analysis, PKD2L1 structures are colored in cyan, green, or yellow according to different domains, and PKD2 or closed-state PKD2L1 model are colored in gray. a The channel passage of PKD2L1 (left) or PKD2 (right, 5T4D) is indicated by purple dots in the center of two diagonal protomers (pore region from chain A and C, polycystin domain from chain B and D) in each channel (with radius smaller than 1.15 Å colored red, between 1.15 and 2.3 Å colored green). The position of selectivity filter is set as the origin of the y-axis. b Pore radii of PKD2L1 (red) and PKD2 (black; 5T4D) along the ion-conducting pathway calculated by HOLE program. c Superimposed examinations between the pore domains of PKD2L1 and PKD2 (only two S5-PH-S6 of diagonal protomers are shown). d Comparison of the selective filter/upper gate between PKD2L1 and PKD2. To emphasize the difference, the two structures of PKD2L1 (cyan) and PKD2 (gray) were superimposed relative to pore helices PH1 and PH2. The constriction site at the upper gate is G522 (PKD2L1) or L641 (PKD2), respectively. Corresponding to PKD2L1 residues, the residue names and numbers in PKD2 are shown in gray immediately after the slash, throughout this study when applicable (In the case of closed-state PKD2L1 model, the respective residue names and numbers in PKD2 are shown in gray within parentheses). e S6 segments of PKD2L1 and PKD2 adopt different conformations. A high-energy π-helix can be witnessed in PKD2 while PKD2L1 only gets a normal α-helix. The absence of this π-helix in PKD2L1 accompanies the C-terminal part of S6 to bend away from the permeation pathway and to shift one residue towards the cytosol. Red arrows emphasize the discrepancies with respect to side chains of marked residues. f Comparison of the lower gate between PKD2L1 and PKD2. Two structures were superimposed similarly as in c. The constriction site at the lower gate is I560 (PKD2L1) or L677 (PKD2), respectively. The counterclockwise red arrows emphasize the comparative differences from PKD2 to PKD2L1

Cryo-EM structure of the polycystic kidney disease-like channel PKD2L1

Nat Commun. 2018;9:1192.