Fig 2: Role of PE and TM3 in ion conduction in hTMEM87A channel activity.a 2D histogram of distances (dP and dR2-Cent) for five MD trajectories (5 × 1 μs from system Sp*/L). dP and dR2-Cent are the distances from the phosphorus atom and the center of mass of the R2-fatty acid chain to the smallest-moment principal axis (Pz) of TMD, respectively. PE in cryo-EM structure (red) and seven highly populated states of PE are labeled (from S1 to S7). b Variations of distances of dP and dR2-Cent as a function of time along one trajectory. States of S4, S3, and S1 are indicated by horizontal lines. c The conformational snapshots of PE in seven different states (S1–S7). PE from cryo-EM structure (pink) and MD simulations are displayed as sticks [the phosphorus atom (orange), R1-fatty acid chain (light blue), and R2-fatty acid chain (teal)]. Dashed lines indicate Pz of TMD. Calculated distances of P and R2-Cent are indicated. Cyan and yellow colored circles represent hydrophilic and hydrophobic cavities in TMD, respectively. d, e Cross-sectional view of hTMEM87 WT and A308M. The A308M, which blocks the PE chain from entering the inner cavity, is highlighted in red. A modeled lipid in A308M is shown as a pink stick. f Current density measured at −150 mV for hTMEM87A WT and A308M (bottom, n = 5 WT and n = 10 for A308M). g Close-up view of lipid binding site in hTMEM87A A308M. h Voltage-sensing TM4 of TRIC-B1 (left, PDB: 5EGI) and potential voltage sensor in TM3 of TMEM87A (right). The conserved basic residues (cyan), nearby acidic residues (yellow), and phospholipids (pink) are shown as sticks. i Current density measured at −150 mV for hTMEM87A WT (n = 5) and mutants on either ends of TM3 (n = 7 for E288R, and n = 6 for AAA). j Water-accessible cavities (yellow surfaces) with putative ion-pathway (red arrow). PE is omitted to show the unblocked lower hydrophobic cavity. Potential voltage-sensing helix TM3 and conserved basic residues are shown as cyan. Data were presented as the mean ± SEM. Statistical analyses were performed using a two-tailed unpaired t-test in (f) (t = 4.605, df = 13); one-way ANOVA followed by Dunnett’s multiple comparisons test (i) (F(2,15) = 24.74). Source data and exact p values are provided as a Source Data file.

Fig 3: Cryo-EM structure and structural feature of human TMEM87A.a Cryo-EM density map of hTMEM87A, colored in slate gray. The density of the micelle (contoured at 0.161σ) is presented as light gray. b Overall structure of hTMEM87A, with ELD (light gray) and TMD [rainbow color from TM1 (red) to TM7 (purple)]. Disulfide bridges (orange, C74–C128, and C89–C431) and N-linked glycans (green, N62, N79, and N127) are shown as sticks. PE and cholesterol are indicated as pink and cyan sticks, respectively. c Topology of hTMEM87A. ELD consists of two α-helices and seven β-strands arranged in an anti-parallel β-sandwich. The secondary structure elements (cylinder for helix and arrow for strand) are colored as in (b). Disulfide bonds are shown as an orange line. Dashed lines denote regions where density was insufficient for model building. d Two different views of the vertical cross-section of the PE-binding pocket in TMD. The electrostatic surface potential of the central cavity is shown. The upper hydrophilic and lower hydrophobic cavities are indicated as cyan and yellow dashed circles, respectively. e Open-book views of the PE-binding pocket and the interaction details. Interaction residues with PE are shown as sticks. The hydrogen and ionic bonds are depicted as a dashed line. Cyan and yellow colored circles represent hydrophilic and hydrophobic cavities in TMD, respectively. f Structural comparison of hTMEM87A TMD with other seven transmembranes (7TM) proteins ChRmine (PDB:7W9W, pale green), Wntless (PDB:7DRT, cyan), and Glucagon receptor (PDB:5YQZ, light purple), shown as a side view (top) and top view (bottom). In the top view, ELD (hTMEM87A), luminal domain (LD, Wntless), and extracellular domain (ECD, glucagon receptor) are omitted for clarity. PE in hTMEM87A, ATR in ChRmine, and Phosphatidylcholine (PC) in Wntless are displayed as pink, cyan, and lime sticks, respectively. g Superimposition of hTMEM87A TMD and TM region of ChRmine (pale green), Wntless (cyan), or glucagon receptor (light purple). The view is a 90° rotation view of (b). along the y-axis to show the lateral opening between TM5 and TM6 of hTMEM87A TMD.

Fig 4: TMEM87A regulates Golgi pH in human astrocytes and mediates voltage- and pH-dependent, inwardly rectifying cationic currents in CHO-K1 cells.a Colocalization of TMEM87A with the Golgin-97, Golgi marker, in cultured human astrocytes. b Comparison of resting Golgi luminal pH and buffer capacities under the absence and presence of 50 mM NH4Cl in Scrambled (gray, n = 14 cells) or TMEM87A shRNA (blue, n = 18 cells) transfected cultured human astrocytes expressing B4GALT1-RpHluorin. Arrows indicate time points in (c, d). c Golgi resting pH values. d Golgi pH values after treating the 50 mM NH4Cl at 30 s. c, d n = 21 cells for Scrambled and n = 18 cells for TMEM87A shRNA. e Schematic diagram of whole-cell patch-clamp recording from TMEM87A WT or TMEM87A-AAA (a.a. 318–320) transfected CHO-K1 cell. Inset: fluorescence image of EGFP-tagged TMEM87A. f Averaged I-V relationship from Control (gray), TMEM87A WT (pink), or TMEM87A-AAA (blue) transfected cells under voltage-ramp protocol (from +100 to −150 mV). g, h Current densities measured at −150 mV in (g) and +100 mV in (h). i The rectification index is calculated as the absolute ratio of amplitude at −150 mV over at +100 mV. g–i n = 27 cells for Control, n = 16 cells for TMEM87A WT, or n = 12 cell for TMEM87A-AAA. j Representative currents from Control and TMEM87A WT transfected cells under voltage-step protocol (from +100 mV to −150 mV, 25 mV step). k Averaged I-V relationship from TMEM87A WT transfected cells with bath solutions containing Na+, NMDG+, K+, or Cs+. l, m Current densities measured at −150 mV in (l) and +100 mV in (m). k–m n = 21 cells for Na+ n = 8 cells for NMDG+, n = 10 cells for K+, n = 8 for Cs+. n Reversal potentials measured from TMEM87A WT transfected cells with bath solutions containing Na+ (n = 13 cells), K+ (n = 10 cells), or Cs+ (n = 8 cells). o Relative permeability ratio of Na+ to K+ (PK+/PNa+, n = 10 cells) or Cs+ (PCs+/PNa+,n = 8 cells). p Representative I-V relationship from TMEM87A WT transfected cell with or without gluconate in the bath solution. q Dose-response curve for percentage currents at −150 mV for gluconate concentrations (n = 5 cells). r Representative I-V relationship from TMEM87A WT transfected cell under various pH. s Normalized currents at −150 mV under various pH, normalized to current at pH 7.3 (n = 7 cells). Data were presented as the mean ± SEM. Statistical analyses were performed using two-tailed unpaired t-test in (c) (t = 8.453, df = 37); two-tailed unpaired t-test with Welch’s test (d) (t = 2.189, df = 37); Kruskal–Wallis test followed by Dunn’s multiple comparisons test in g (H = 25.34), h (H = 21.98), i (H = 15.61); one-way ANOVA followed by Dunnett’s multiple comparisons test in l (F(3,43) = 44.10), m (F(3,43) = 2.164), and n (F(2,28) = 7.552). Source data and exact p values are provided as a Source Data file.