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- PDB-5ydz: structure of endo-lysosomal TRPML1 channel inserting into amphipo... -

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Entry
Database: PDB / ID: 5ydz
Titlestructure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1
Componentsmammalian endo-lysosomal TRPML1 channel
KeywordsMEMBRANE PROTEIN / mTRPML1 / mucolipidosis type IV / structual comparisons / combined regulation mechanism
Function/homologyTransferrin 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
Specimen sourceMus musculus / House mouse / mammal /
MethodElectron microscopy (5.8 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsYang, M. / Gao, N.
CitationJournal: 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
SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2017 / Release: Dec 27, 2017

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Assembly

Deposited unit
A: mammalian endo-lysosomal TRPML1 channel
B: mammalian endo-lysosomal TRPML1 channel
C: mammalian endo-lysosomal TRPML1 channel
D: mammalian endo-lysosomal TRPML1 channel


Theoretical massNumber of molelcules
Total (without water)262,2944
Polyers262,2944
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
mammalian endo-lysosomal TRPML1 channel / Mucolipidin / Transient receptor potential-mucolipin 1 / TRPML1


Mass: 65573.617 Da / Num. of mol.: 4 / Source: (gene. exp.) Mus musculus / House mouse / mammal / / Gene: Mcoln1 / Production host: Homo sapiens / References: UniProt:Q99J21

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: mammalian endo-lysosomal TRPML1 channel inserting into amphipol
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus
Source (recombinant)Organism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: Amorphous ice
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 2 / Category: RECONSTRUCTION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 167000 / Symmetry type: POINT

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