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. 2017 Oct 19;550(7676):415-418.
doi: 10.1038/nature24035. Epub 2017 Oct 11.

Structure of mammalian endolysosomal TRPML1 channel in nanodiscs

Qingfeng Chen  1   2   3 , Ji She  1   2 , Weizhong Zeng  1   2   3 , Jiangtao Guo  1   2 , Haoxing Xu  4 , Xiao-Chen Bai  2 , Youxing Jiang  1   2   3
Affiliations

Structure of mammalian endolysosomal TRPML1 channel in nanodiscs

Qingfeng Chen et al. Nature. .

Abstract

Transient receptor potential mucolipin 1 (TRPML1) is a cation channel located within endosomal and lysosomal membranes. Ubiquitously expressed in mammalian cells, its loss-of-function mutations are the direct cause of type IV mucolipidosis, an autosomal recessive lysosomal storage disease. Here we present the single-particle electron cryo-microscopy structure of the mouse TRPML1 channel embedded in nanodiscs. Combined with mutagenesis analysis, the TRPML1 structure reveals that phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2) binds to the N terminus of the channel-distal from the pore-and the helix-turn-helix extension between segments S2 and S3 probably couples ligand binding to pore opening. The tightly packed selectivity filter contains multiple ion-binding sites, and the conserved acidic residues form the luminal Ca2+-blocking site that confers luminal pH and Ca2+ modulation on channel conductance. A luminal linker domain forms a fenestrated canopy atop the channel, providing several luminal ion passages to the pore and creating a negative electrostatic trap, with a preference for divalent cations, at the luminal entrance. The structure also reveals two equally distributed S4-S5 linker conformations in the closed channel, suggesting an S4-S5 linker-mediated PtdInsP2 gating mechanism among TRPML channels.

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Figures

Figure 1
Figure 1
Overall structure of TRPML1. a, Side view of 3-D reconstruction of TRPML1 in nanodisc (grey belt). Channel subunits are colored individually with lipid density in grey. b, Side view of cartoon representation of TRPML1 structure. N-acetylglucosamine (NAG) molecules are rendered as sticks. c, Cytosolic view of the channel. d, Structure of a single subunit in the same orientation as the cyan-colored subunit in b.
Figure 2
Figure 2
Structure of S1-S4 region and the PIP2 binding site. a, S1-S4 domain (blue) of the front subunit. The two cytosolic extensions are colored differently - magenta for H1 & H2 and green for the H3-turn-H4 between S2 and S3. Inset shows inter-subunit contact between S4 helix (blue) and the neighboring S5 (pink). b, Zoomed-in view of the poly-basic domain and the interactions between H1 and H3 helix.
Figure 3
Figure 3
Ion conduction pathway of TRPML1. a, Ion conduction pore of TRPML1 with front and rear subunits removed for clarity. Central pathway is marked with dotted mesh. Insets are zoomed-in views of the bundle crossing with atom-to-atom distances in Å and the packing between S5 and S6. π-helix on S6 is colored in red. b, Pore radius along the central axis. c, Zoomed-in view of the selectivity filter with atom-to-atom distances in Å. S0 density is modeled as Na+ (red sphere). d. Top view of the selectivity filter showing H-bonding networks between Asp471 side chain and backbone nitrogen atoms of neighboring filter residues. e, Top view of the luminal linker domains in tetramer. Three acidic residues on the luminal pore loop (labeled as loop) form the narrowest part of the central hole. f, Side view of the funnel shaped central hole and the open central court just above the filter. Front and rear subunits are removed for clarity. The luminal pore loop is colored red. g, Cross section through the channel showing the surface electrostatic potential along the ion conduction pathway. The open court at the luminal entrance is accessible by multiple luminal ion passages indicated by arrows.
Figure 4
Figure 4
Alternative conformations of TRPML1 in closed state. a, Superposition between -closed I (purple) and closed II (green) states with H1 and H2 helices omitted for clarity. Arrows indicate the movement of S4-S5 linker. b, Zoomed-in view of the superposition for one subunit. c, Inter-subunit interactions between N-terminus of the linker and N-terminus of the neighboring S5 in closed I state at the location marked by the purple box in b. d, Interactions between partially unfolded linker and H4 helix at the location marked by the green box in b. e, Proposed working model for PI(3,5)P2 activation. Arrows indicate proposed movements upon ligand binding.
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References

    1. Cheng X, Shen D, Samie M, Xu H. Mucolipins: Intracellular TRPML1-3 channels. FEBS Lett. 2010;584:2013–2021. doi: 10.1016/j.febslet.2009.12.056. - DOI - PMC - PubMed
    1. Dong XP, et al. The type IV mucolipidosis-associated protein TRPML1 is an endolysosomal iron release channel. Nature. 2008;455:992–996. doi: 10.1038/nature07311. - DOI - PMC - PubMed
    1. Bargal R, et al. Identification of the gene causing mucolipidosis type IV. Nat Genet. 2000;26:118–123. doi: 10.1038/79095. - DOI - PubMed
    1. Bassi MT, et al. Cloning of the gene encoding a novel integral membrane protein, mucolipidin and identification of the two major founder mutations causing mucolipidosis type IV. Am J Hum Genet. 2000;67:1110–1120. doi: 10.1016/S0002-9297(07)62941-3. - DOI - PMC - PubMed
    1. Nilius B, Owsianik G, Voets T, Peters JA. Transient receptor potential cation channels in disease. Physiol Rev. 2007;87:165–217. doi: 10.1152/physrev.00021.2006. - DOI - PubMed

Methods References

    1. Zheng SQ, et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods. 2017;14:331–332. doi: 10.1038/nmeth.4193. - DOI - PMC - PubMed
    1. Zhang K. Gctf: Real-time CTF determination and correction. J Struct Biol. 2016;193:1–12. doi: 10.1016/j.jsb.2015.11.003. - DOI - PMC - PubMed
    1. Scheres SH. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol. 2012;180:519–530. doi: 10.1016/j.jsb.2012.09.006. - DOI - PMC - PubMed
    1. Bai XC, Rajendra E, Yang G, Shi Y, Scheres SH. Sampling the conformational space of the catalytic subunit of human gamma-secretase. Elife. 2015;4 doi: 10.7554/eLife.11182. - DOI - PMC - PubMed
    1. Kucukelbir A, Sigworth FJ, Tagare HD. Quantifying the local resolution of cryo-EM density maps. Nat Methods. 2014;11:63–65. doi: 10.1038/nmeth.2727. - DOI - PMC - PubMed

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