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- PDB-9y7o: Cryo-EM structure of PI(3,5)P2 and ML-SA1 bound full-length mouse... -

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Basic information

Entry
Database: PDB / ID: 9y7o
TitleCryo-EM structure of PI(3,5)P2 and ML-SA1 bound full-length mouse TRPML2 channel in lipid nanodisc, closed I
ComponentsMucolipin-2
KeywordsMEMBRANE PROTEIN / Cation channel
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 / adaptive immune response / recycling endosome membrane / 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
Chem-AQV / Chem-EUJ / Mucolipin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsPark, S. / Yang, J.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mucolipin-2
C: Mucolipin-2
B: Mucolipin-2
D: Mucolipin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,51812
Polymers262,0824
Non-polymers4,4368
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Mucolipin-2 / Transient receptor potential channel mucolipin 2 / TRPML2


Mass: 65520.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mcoln2 / Production host: Homo sapiens (human) / References: UniProt: Q8K595
#2: Chemical
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


Mass: 746.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AQV / 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione


Mass: 362.422 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H22N2O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Full length mouse homotetrameric TRPML2 channel in lipid nanodisc
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 23.52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121638 / Symmetry type: POINT
RefinementHighest resolution: 3.01 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00515728
ELECTRON MICROSCOPYf_angle_d0.50221300
ELECTRON MICROSCOPYf_dihedral_angle_d6.9862088
ELECTRON MICROSCOPYf_chiral_restr0.0412412
ELECTRON MICROSCOPYf_plane_restr0.0032580

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