5WPV

Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs at 3.59 Angstrom resolution

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc

  • Deposited: 2017-08-07 Released: 2017-10-18 
  • Deposition Author(s): Chen, Q., She, J., Guo, J., Bai, X., Jiang, Y.
  • Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR), Howard Hughes Medical Institute (HHMI), Welch Foundation, Cancer Prevention and Research Institute of Texas (CPRIT), Virginia Murchison Linthicum Scholar in Medical Research fund

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 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

Structure of mammalian endolysosomal TRPML1 channel in nanodiscs.

Chen, Q.She, J.Zeng, W.Guo, J.Xu, H.Bai, X.C.Jiang, Y.

(2017) Nature 550: 415-418

  • DOI: 10.1038/nature24035
  • Primary Citation of Related Structures:  
    5WPV, 5WPQ, 5WPT

  • PubMed Abstract: 
  • Transient receptor potential mucolipin 1 (TRPML1) is a cation channel located within endosomal and lysosomal membranes. Ubiquitously expressed in mammalian cells, its loss-of-function mutations are the direct cause of type IV mucolipidosis, an autosomal recessive lysosomal storage disease ...

    Transient receptor potential mucolipin 1 (TRPML1) is a cation channel located within endosomal and lysosomal membranes. Ubiquitously expressed in mammalian cells, its loss-of-function mutations are the direct cause of type IV mucolipidosis, an autosomal recessive lysosomal storage disease. Here we present the single-particle electron cryo-microscopy structure of the mouse TRPML1 channel embedded in nanodiscs. Combined with mutagenesis analysis, the TRPML1 structure reveals that phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P 2 ) binds to the N terminus of the channel-distal from the pore-and the helix-turn-helix extension between segments S2 and S3 probably couples ligand binding to pore opening. The tightly packed selectivity filter contains multiple ion-binding sites, and the conserved acidic residues form the luminal Ca 2+ -blocking site that confers luminal pH and Ca 2+ modulation on channel conductance. A luminal linker domain forms a fenestrated canopy atop the channel, providing several luminal ion passages to the pore and creating a negative electrostatic trap, with a preference for divalent cations, at the luminal entrance. The structure also reveals two equally distributed S4-S5 linker conformations in the closed channel, suggesting an S4-S5 linker-mediated PtdInsP 2 gating mechanism among TRPML channels.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mucolipin-1A, B, C, D592Mus musculusMutation(s): 0 
Gene Names: Mcoln1Trpml1
Membrane Entity: Yes 
UniProt
Find proteins for Q99J21 (Mus musculus)
Explore Q99J21 
Go to UniProtKB:  Q99J21
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, G, H2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 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 Center for Research Resources (NIH/NCRR)United StatesGM079179
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesNS062792
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesAR060837
Howard Hughes Medical Institute (HHMI)United States--
Welch FoundationUnited StatesI-1578
Cancer Prevention and Research Institute of Texas (CPRIT)United States--
Virginia Murchison Linthicum Scholar in Medical Research fundUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references
  • Version 1.2: 2019-04-24
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary