|Entry||Database: EMDB / ID: 6823|
|Title||structure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1|
|Map data||Amphipol A8-35 state 1|
|Sample||mammalian endo-lysosomal TRPML1 channel inserting into amphipol|
|Function/homology||Transferrin endocytosis and recycling / cation transmembrane transport / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / ligand-gated calcium channel activity / NAADP-sensitive calcium-release channel activity / TRP channels / cellular response to pH / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / cation channel activity ...Transferrin endocytosis and recycling / cation transmembrane transport / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / ligand-gated calcium channel activity / NAADP-sensitive calcium-release channel activity / TRP channels / cellular response to pH / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / cation channel activity / phagocytic cup / autophagosome maturation / late endosome membrane / calcium ion transmembrane transport / cell projection / cellular response to calcium ion / endosomal transport / lysosomal membrane / phagocytic vesicle membrane / late endosome / adaptive immune response / protein homotetramerization / receptor complex / lysosome / lipid binding / membrane / integral component of membrane / plasma membrane / cytosol / Mucolipin-1|
Function and homology information
|Source||Mus musculus / House mouse / mammal /|
|Method||Cryo EM / single particle reconstruction / 5.8 Å resolution|
|Authors||Yang M / Gao N|
|Citation||Journal: Protein Cell / Year: 2017|
Title: Cryo-EM structures of the mammalian endo-lysosomal TRPML1 channel elucidate the combined regulation mechanism.
Authors: Sensen Zhang / Ningning Li / Wenwen Zeng / Ning Gao / Maojun Yang
Abstract: TRPML1 channel is a non-selective group-2 transient receptor potential (TRP) channel with Ca permeability. Located mainly in late endosome and lysosome of all mammalian cell types, TRPML1 is ...TRPML1 channel is a non-selective group-2 transient receptor potential (TRP) channel with Ca permeability. Located mainly in late endosome and lysosome of all mammalian cell types, TRPML1 is indispensable in the processes of endocytosis, membrane trafficking, and lysosome biogenesis. Mutations of TRPML1 cause a severe lysosomal storage disorder called mucolipidosis type IV (MLIV). In the present study, we determined the cryo-electron microscopy (cryo-EM) structures of Mus musculus TRPML1 (mTRPML1) in lipid nanodiscs and Amphipols. Two distinct states of mTRPML1 in Amphipols are added to the closed state, on which could represent two different confirmations upon activation and regulation. The polycystin-mucolipin domain (PMD) may sense the luminal/extracellular stimuli and undergo a "move upward" motion during endocytosis, thus triggering the overall conformational change in TRPML1. Based on the structural comparisons, we propose TRPML1 is regulated by pH, Ca, and phosphoinositides in a combined manner so as to accommodate the dynamic endocytosis process.
|Validation Report||PDB-ID: 5ydz|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 15, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017|
Downloads & links
|File||emd_6823.map.gz (map file in CCP4 format, 1373 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.64 Å|
CCP4 map header:
-Entire mammalian endo-lysosomal TRPML1 channel inserting into amphipol
|Entire||Name: mammalian endo-lysosomal TRPML1 channel inserting into amphipol|
Number of components: 2
-Component #1: cellular-component, mammalian endo-lysosomal TRPML1 channel inser...
|Cellular-component||Name: mammalian endo-lysosomal TRPML1 channel inserting into amphipol|
Recombinant expression: No
|Source||Species: Mus musculus / House mouse / mammal /|
|Source (engineered)||Expression System: Homo sapiens / / human|
-Component #2: protein, mammalian endo-lysosomal TRPML1 channel
|Protein||Name: mammalian endo-lysosomal TRPML1 channel / Recombinant expression: No|
|Mass||Theoretical: 65.573617 kDa|
|Source (engineered)||Expression System: Mus musculus / House mouse / mammal /|
|Specimen||Specimen state: particle / Method: Cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 167000|
|3D reconstruction||Software: RELION / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF|
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