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- EMDB-6825: mammalian endo-lysosomal TRPML1 channel inserting into amphipol -

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Basic information

Entry
Database: EMDB / ID: 6825
Titlemammalian endo-lysosomal TRPML1 channel inserting into amphipol
Map dataamphipol state 3
Samplemammalian endo-lysosomal TRPML1 channel inserting into amphipol
  • mammalian endo-lysosomal TRPML1 channel
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
SourceMus musculus / House mouse / mammal /
MethodCryo EM / single particle reconstruction / 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
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 ReportPDB-ID: 5ye2

SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5ye2
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

emd_6825.png

Downloads & links

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Map

Fileemd_6825.map.gz (map file in CCP4 format, 1373 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
70 pix
2.64 Å/pix.
= 184.8 Å		70 pix
2.64 Å/pix.
= 184.8 Å		70 pix
2.64 Å/pix.
= 184.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.64 Å
Density

Histogram

Histogram (log scale)
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum-4.1359735 - 8.653038
Average (Standard dev.)-4.4601973E-7 (1.0000001)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions707070
Origin000
Limit696969
Spacing707070
CellA=B=C: 184.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.642.642.64
M x/y/z707070
origin x/y/z0.0000.0000.000
length x/y/z184.800184.800184.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707070
D min/max/mean-4.1368.653-0.000

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Supplemental data

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Sample components

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Entire mammalian endo-lysosomal TRPML1 channel inserting into amphipol

EntireName: mammalian endo-lysosomal TRPML1 channel inserting into amphipol
Number of components: 2

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Component #1: cellular-component, mammalian endo-lysosomal TRPML1 channel inser...

Cellular-componentName: mammalian endo-lysosomal TRPML1 channel inserting into amphipol
Recombinant expression: No
SourceSpecies: Mus musculus / House mouse / mammal /
Source (engineered)Expression System: Homo sapiens / / human

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Component #2: protein, mammalian endo-lysosomal TRPML1 channel

ProteinName: mammalian endo-lysosomal TRPML1 channel / Recombinant expression: No
MassTheoretical: 65.573617 kDa
Source (engineered)Expression System: Mus musculus / House mouse / mammal /

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 167000
3D reconstructionSoftware: RELION / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

5ye2

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