9EKY | pdb_00009eky

(+)ML-SI3 bound TRPML2 in a pre-open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

TRPML2 in distinct states reveals the activation and modulation principles of the TRPML family.

Schmiege, P.Jaslan, D.Fine, M.Sadanandan, N.P.Hatton, A.Elghobashi-Meinhardt, N.Grimm, C.Li, X.

(2025) Nat Commun 16: 5325-5325

  • DOI: https://doi.org/10.1038/s41467-025-60710-8
  • Primary Citation of Related Structures:  
    9EKS, 9EKT, 9EKU, 9EKV, 9EKW, 9EKX, 9EKY, 9EKZ, 9EL0, 9EL1

  • PubMed Abstract: 

    TRPML2 activity is critical for endolysosomal integrity and chemokine secretion, and can be modulated by various ligands. Interestingly, two ML-SI3 isomers regulate TRPML2 oppositely. The molecular mechanism underlying this unique isomeric preference as well as the TRPML2 agonistic mechanism remains unknown. Here, we present six cryo-EM structures of human TRPML2 in distinct states revealing that the π-bulge of the S6 undergoes a π-α transition upon agonist binding, highlighting the remarkable role of the π-bulge in ion channel regulation. Moreover, we identify that PI(3,5)P 2 allosterically affects the pose of ML2-SA1, a TRPML2 specific activator, resulting in an open channel without the π-α transition. Functional and structural studies show that mutating the S5 of TRPML1 to that of TRPML2 enables the mutated TRPML1 to be activated by (+)ML-SI3 and ML2-SA1. Thus, our work elucidates the activation mechanism of TRPML channels and paves the way for the development of selective TRPML modulators.


  • Organizational Affiliation
    • Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mucolipin-2
A, B, C, D
566Homo sapiensMutation(s): 0 
Gene Names: MCOLN2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZK6 (Homo sapiens)
Explore Q8IZK6 
Go to UniProtKB:  Q8IZK6
PHAROS:  Q8IZK6
GTEx:  ENSG00000153898 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IZK6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM149533

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 2.0: 2026-01-07
    Changes: Atomic model, Data collection, Database references