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- PDB-5ye1: structure of endo-lysosomal TRPML1 channel inserting into amphipo... -

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Basic information

Entry
Database: PDB / ID: 5ye1
Titlestructure of endo-lysosomal TRPML1 channel inserting into amphipol: state 2
ComponentsMucolipin-1MCOLN1
KeywordsMEMBRANE PROTEIN / mTRPML1 / mucolipidosis type IV / structual comparisons / combined regulation mechanism
Function / homologyTransferrin endocytosis and recycling / TRP channels / Polycystin cation channel / Mucolipin / Polycystin cation channel, PKD1/PKD2 / cation transmembrane transport / ligand-gated calcium channel activity / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / intracellular vesicle / NAADP-sensitive calcium-release channel activity ...Transferrin endocytosis and recycling / TRP channels / Polycystin cation channel / Mucolipin / Polycystin cation channel, PKD1/PKD2 / cation transmembrane transport / ligand-gated calcium channel activity / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / intracellular vesicle / NAADP-sensitive calcium-release channel activity / cellular response to pH / cation channel activity / phagocytic cup / autophagosome maturation / release of sequestered calcium ion into cytosol / late endosome membrane / calcium ion transmembrane transport / cell projection / endosomal transport / cellular response to calcium ion / lysosomal membrane / phagocytic vesicle membrane / late endosome / protein homotetramerization / receptor complex / adaptive immune response / lysosome / lipid binding / membrane / integral component of membrane / plasma membrane / cytosol / Mucolipin-1
Function and homology information
Specimen sourceMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.8 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2017 / Release: Dec 27, 2017

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Structure visualization

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Assembly

Deposited unit
A: Mucolipin-1
B: Mucolipin-1
C: Mucolipin-1
D: Mucolipin-1


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
Mucolipin-1 / MCOLN1 / Mucolipidin / Transient receptor potential-mucolipin 1 / TRPML1


Mass: 65573.617 Da / Num. of mol.: 4 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mcoln1 / Production host: Homo sapiens (human) / 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 reconstruction

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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 (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
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 FIELDBright-field microscopy
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: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 167000 / Symmetry type: POINT

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