6E7P

cryo-EM structure of human TRPML1 with PI35P2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structural basis for PtdInsP2-mediated human TRPML1 regulation.

Fine, M.Schmiege, P.Li, X.

(2018) Nat Commun 9: 4192-4192

  • DOI: 10.1038/s41467-018-06493-7
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Transient receptor potential mucolipin 1 (TRPML1), a lysosomal channel, maintains the low pH and calcium levels for lysosomal function. Several small molecules modulate TRPML1 activity. ML-SA1, a synthetic agonist, binds to the pore region and phosph ...

    Transient receptor potential mucolipin 1 (TRPML1), a lysosomal channel, maintains the low pH and calcium levels for lysosomal function. Several small molecules modulate TRPML1 activity. ML-SA1, a synthetic agonist, binds to the pore region and phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P 2 ), a natural lipid, stimulates channel activity to a lesser extent than ML-SA1; moreover, PtdIns(4,5)P 2 , another natural lipid, prevents TRPML1-mediated calcium release. Notably, PtdIns(3,5)P 2 and ML-SA1 cooperate further increasing calcium efflux. Here we report the structures of human TRPML1 at pH 5.0 with PtdIns(3,5)P 2 , PtdIns(4,5)P 2 , or ML-SA1 and PtdIns(3,5)P 2 , revealing a unique lipid-binding site. PtdIns(3,5)P 2 and PtdIns(4,5)P 2 bind to the extended helices of S1, S2, and S3. The phosphate group of PtdIns(3,5)P 2 induces Y355 to form a π-cation interaction with R403, moving the S4-S5 linker, thus allosterically activating the channel. Our structures and electrophysiological characterizations reveal an allosteric site and provide molecular insight into how lipids regulate TRP channels.


    Organizational Affiliation

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. xiaochun.li@utsouthwestern.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mucolipin-1
A, B, C, D
580Homo sapiensMutation(s): 0 
Gene Names: MCOLN1ML4MSTP080
Find proteins for Q9GZU1 (Homo sapiens)
Go to UniProtKB:  Q9GZU1
NIH Common Fund Data Resources
PHAROS  Q9GZU1
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HZ7
Query on HZ7

Download CCD File 
A, B, C, D
(1R,2S,3S,4R,5S,6R)-5-{[(R)-[(2R)-2,3-bis{[(1S)-1-hydroxyoctyl]oxy}propoxy](hydroxy)phosphoryl]oxy}-2,4,6-trihydroxycyclohexane-1,3-diyl bis[dihydrogen (phosphate)]
C25 H53 O19 P3
YMIVTWICVQDVIN-OZVNAFTMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-07-27 
  • Released Date: 2018-11-28 
  • Deposition Author(s): Schmiege, P., Li, X.

Revision History 

  • Version 1.0: 2018-11-28
    Type: Initial release