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- EMDB-8764: Cryo-electron microscopy structure of a TRPML3 ion channel -

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Basic information

Entry
Database: EMDB / ID: EMD-8764
TitleCryo-electron microscopy structure of a TRPML3 ion channel
Map dataTRPML3 ion channel
Sample
  • Complex: Transient Receptor Potential Mucolipin 3
    • Protein or peptide: Mucolipin-3 isoform 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: SODIUM ION
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water
Keywordstransient receptor potential channel / mucolipin / ion channel / membrane transport / TRPML / TRP channel / calcium channel / PIP2 / PI(3 / 5)P2 / lipid-gated channel / mucolipidosis / lysosomal ion channel / lysosome / TRANSPORT PROTEIN
Function / homology
Function and homology information


stereocilium membrane / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / NAADP-sensitive calcium-release channel activity / monoatomic anion channel activity / phosphatidylinositol-3,5-bisphosphate binding / sodium channel activity / monoatomic cation transmembrane transport / autophagosome membrane / potassium channel activity / late endosome membrane ...stereocilium membrane / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / NAADP-sensitive calcium-release channel activity / monoatomic anion channel activity / phosphatidylinositol-3,5-bisphosphate binding / sodium channel activity / monoatomic cation transmembrane transport / autophagosome membrane / potassium channel activity / late endosome membrane / early endosome membrane / protein homotetramerization / lysosomal membrane / identical protein binding / membrane
Similarity search - Function
: / Mucolipin / : / Mucolipin, extracytosolic domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel
Similarity search - Domain/homology
Biological speciesCallithrix jacchus (white-tufted-ear marmoset)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsHirschi M / Herzik MA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS097241 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)DP2EB020402 United States
CitationJournal: Nature / Year: 2017
Title: Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3.
Authors: Marscha Hirschi / Mark A Herzik / Jinhong Wie / Yang Suo / William F Borschel / Dejian Ren / Gabriel C Lander / Seok-Yong Lee /
Abstract: The modulation of ion channel activity by lipids is increasingly recognized as a fundamental component of cellular signalling. The transient receptor potential mucolipin (TRPML) channel family ...The modulation of ion channel activity by lipids is increasingly recognized as a fundamental component of cellular signalling. The transient receptor potential mucolipin (TRPML) channel family belongs to the TRP superfamily and is composed of three members: TRPML1-TRPML3. TRPMLs are the major Ca-permeable channels on late endosomes and lysosomes (LEL). They regulate the release of Ca from organelles, which is important for various physiological processes, including organelle trafficking and fusion. Loss-of-function mutations in the MCOLN1 gene, which encodes TRPML1, cause the neurodegenerative lysosomal storage disorder mucolipidosis type IV, and a gain-of-function mutation (Ala419Pro) in TRPML3 gives rise to the varitint-waddler (Va) mouse phenotype. Notably, TRPML channels are activated by the low-abundance and LEL-enriched signalling lipid phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P), whereas other phosphoinositides such as PtdIns(4,5)P, which is enriched in plasma membranes, inhibit TRPMLs. Conserved basic residues at the N terminus of the channel are important for activation by PtdIns(3,5)P and inhibition by PtdIns(4,5)P. However, owing to a lack of structural information, the mechanism by which TRPML channels recognize PtdIns(3,5)P and increase their Ca conductance remains unclear. Here we present the cryo-electron microscopy (cryo-EM) structure of a full-length TRPML3 channel from the common marmoset (Callithrix jacchus) at an overall resolution of 2.9 Å. Our structure reveals not only the molecular basis of ion conduction but also the unique architecture of TRPMLs, wherein the voltage sensor-like domain is linked to the pore via a cytosolic domain that we term the mucolipin domain. Combined with functional studies, these data suggest that the mucolipin domain is responsible for PtdIns(3,5)P binding and subsequent channel activation, and that it acts as a 'gating pulley' for lipid-dependent TRPML gating.
History
DepositionJun 8, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseOct 11, 2017-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5w3s
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8764.png

Downloads & links

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Map

FileDownload / File: emd_8764.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPML3 ion channel
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 256 pix.
= 167.68 Å		0.66 Å/pix.
x 256 pix.
= 167.68 Å		0.66 Å/pix.
x 256 pix.
= 167.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.655 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.08215571 - 0.14267515
Average (Standard dev.)0.00058275065 (±0.010049041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 167.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6550.6550.655
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z167.680167.680167.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0820.1430.001

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Supplemental data

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Additional map: TRPML3 ion channel

Fileemd_8764_additional.map
AnnotationTRPML3 ion channel
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TRPML3 ion channel

Fileemd_8764_half_map_1.map
AnnotationTRPML3 ion channel
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TRPML3 ion channel

Fileemd_8764_half_map_2.map
AnnotationTRPML3 ion channel
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transient Receptor Potential Mucolipin 3

EntireName: Transient Receptor Potential Mucolipin 3
Components
  • Complex: Transient Receptor Potential Mucolipin 3
    • Protein or peptide: Mucolipin-3 isoform 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: SODIUM ION
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water

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Supramolecule #1: Transient Receptor Potential Mucolipin 3

SupramoleculeName: Transient Receptor Potential Mucolipin 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Callithrix jacchus (white-tufted-ear marmoset)
Molecular weightTheoretical: 260 KDa

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Macromolecule #1: Mucolipin-3 isoform 1

MacromoleculeName: Mucolipin-3 isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Callithrix jacchus (white-tufted-ear marmoset)
Molecular weightTheoretical: 65.092301 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MANPEIVISS CSSHEEENRC NFNQHTSPSE ELLLEDQMRR KLKFFFMNPC EKFWARGRKP WKLAIQILKI AMVTIQLVLF GLSNQMVVA FKEENTVAFK HLFLKGYIDR MDDTYAVYTQ SDVYDQIIFA VNQYLQLYQV SVGNHAYENK GTDQSAMAIC Q HFYKRGNI ...String:
MANPEIVISS CSSHEEENRC NFNQHTSPSE ELLLEDQMRR KLKFFFMNPC EKFWARGRKP WKLAIQILKI AMVTIQLVLF GLSNQMVVA FKEENTVAFK HLFLKGYIDR MDDTYAVYTQ SDVYDQIIFA VNQYLQLYQV SVGNHAYENK GTDQSAMAIC Q HFYKRGNI YPGNDTFDID PEIETDCFFV EPDEPFHIGT PAENKLNLTL DFHRLLTVEL QFKLKAINLQ TVRHQELPDC YD FTLTITF DNKAHSGRIK ISLDNDISIR ECKDWHVSGS IQKNTHNMMI FDAFVILTCL VSLILCIRSV ISGLQLQQEF VNF FLLHYK KDVSVSDQME FVNGWYIMII ISDILTIIGS ILKMEIQAKS LTSYDVCSIL LGTSTMLVWL GVIRYLGFFA KYNL LILTL QAALPNVIRF CCCAAMIYLG YCFCGWIVLG PYHNKFRSLN MVSECLFSLI NGDDMFATFA KMQQKSYLVW LFSRI YLYS FISLFIYMIL SLFIALITDT YETIKHYQQD GFPETELRTF ISECKDLPNS GKFRLEDDPP VSLFCCCKKS NLEVLF Q

UniProtKB: Mucolipin-3

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 6
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 4 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 12.0 sec. / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104084
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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