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- EMDB-72662: Cryo-EM structure of PI(3,5)P2 and ML-SA1 bound full-length mouse... -

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Basic information

Entry
Database: EMDB / ID: EMD-72662
TitleCryo-EM structure of PI(3,5)P2 and ML-SA1 bound full-length mouse TRPML2 channel in lipid nanodisc, closed I
Map datastructure of PI(3,5)P2 and ML-SA1 bound full-length mouse TRPML2 channel in lipid nanodisc, closed I
Sample
  • Complex: Full length mouse homotetrameric TRPML2 channel in lipid nanodisc
    • Protein or peptide: Mucolipin-2
  • Ligand: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate
  • Ligand: 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione
KeywordsCation channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


macrophage migration / regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of macrophage inflammatory protein 1 alpha production / positive regulation of chemokine (C-C motif) ligand 5 production / NAADP-sensitive calcium-release channel activity / iron ion transmembrane transporter activity / neutrophil migration / TRP channels / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production ...macrophage migration / regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of macrophage inflammatory protein 1 alpha production / positive regulation of chemokine (C-C motif) ligand 5 production / NAADP-sensitive calcium-release channel activity / iron ion transmembrane transporter activity / neutrophil migration / TRP channels / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of chemokine production / protein transport / recycling endosome / recycling endosome membrane / adaptive immune response / innate immune response / membrane / identical protein binding
Similarity search - Function
Mucolipin / : / Mucolipin, extracytosolic domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsPark S / Yang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)RO1EY032880 United States
CitationJournal: To Be Published
Title: Conformational landscape of synergistic activation of mouse TRPML2 channel
Authors: Park S / Yang J
History
DepositionSep 10, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72662.png

Downloads & links

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Map

FileDownload / File: emd_72662.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of PI(3,5)P2 and ML-SA1 bound full-length mouse TRPML2 channel in lipid nanodisc, closed I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.237
Minimum - Maximum-1.4182342 - 2.0826025
Average (Standard dev.)0.008766401 (±0.07403024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_72662_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72662_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full length mouse homotetrameric TRPML2 channel in lipid nanodisc

EntireName: Full length mouse homotetrameric TRPML2 channel in lipid nanodisc
Components
  • Complex: Full length mouse homotetrameric TRPML2 channel in lipid nanodisc
    • Protein or peptide: Mucolipin-2
  • Ligand: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate
  • Ligand: 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione

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Supramolecule #1: Full length mouse homotetrameric TRPML2 channel in lipid nanodisc

SupramoleculeName: Full length mouse homotetrameric TRPML2 channel in lipid nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Mucolipin-2

MacromoleculeName: Mucolipin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 65.520602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPGDEETLDL PAWNRVPDLT WGPHHRSAMA SLDSEVREEC LREDLKFYFM SPCEKYRARR QIPWKLGLQI LKIVMVTTQL VRFGLSNQL VVAFKEDNTV AFKHLFLKGF SGVDEDDYSC SIYTQENTYE SIFFAIKQYR HLKNISLATL GYGESEDNRT G LKVCKQHY ...String:
MPGDEETLDL PAWNRVPDLT WGPHHRSAMA SLDSEVREEC LREDLKFYFM SPCEKYRARR QIPWKLGLQI LKIVMVTTQL VRFGLSNQL VVAFKEDNTV AFKHLFLKGF SGVDEDDYSC SIYTQENTYE SIFFAIKQYR HLKNISLATL GYGESEDNRT G LKVCKQHY KTGAMFSSNE TLNIDSDIET DCIHLDLQVL TTEPEDWAQT SFFRLDFYRL VQVDISFALK GIDLQAVHSR EI PDCYLFQ NTITFDNTAH SGKIKIYLNS EANIEECKNM NISGSTQRST HYLLVFDVFV IMICLASLIL CTRSIVLALR LRK RFLNFF LEKYKQRVCG ADQWEFVNGW YVLVTISDLM TIIGSILKME IKAKKLTNYD VCSILLGTST LFVWVGVIRY LGYF QTYNV LILTMQASLP KVLRFCACAG MIYLGYTFCG WIVLGPYHEK FENLNIVAEC LFSLVNGDDM FATFAQIQQK SILVW LFSR LYLYSFISLF IYMVLSLFIA LITDSYHTIK KYQQHGFPET DLQKFLKESG SKDGYQKQPS ALLSCLCCLR RRRSND HLI LID

UniProtKB: Mucolipin-2

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Macromolecule #2: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bi...

MacromoleculeName: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: EUJ
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-EUJ:
(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate

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Macromolecule #3: 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]eth...

MacromoleculeName: 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione
type: ligand / ID: 3 / Number of copies: 4 / Formula: AQV
Molecular weightTheoretical: 362.422 Da
Chemical component information

ChemComp-AQV:
2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 23.52 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 121638
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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