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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 / TRP channels / Polycystin cation channel / Mucolipin / Polycystin cation channel, PKD1/PKD2 / cation transmembrane transport / intracellular vesicle / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / ligand-gated calcium channel activity / NAADP-sensitive calcium-release channel activity ...Transferrin endocytosis and recycling / TRP channels / Polycystin cation channel / Mucolipin / Polycystin cation channel, PKD1/PKD2 / cation transmembrane transport / intracellular vesicle / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / ligand-gated calcium channel activity / 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 / cellular response to calcium ion / endosomal transport / lysosomal membrane / phagocytic vesicle membrane / late endosome / protein homotetramerization / adaptive immune response / lysosome / receptor complex / lipid binding / membrane / integral component of membrane / plasma membrane / cytosol / Mucolipin-1
Function and homology information
SourceMus musculus (house mouse)
Methodsingle 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 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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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.

Voxel sizeX=Y=Z: 2.64 Å
Density

Histogram

Histogram (log scale)
Contour Level:3.0 (by author), 3 (movie #1):
Minimum - Maximum-4.1359735 - 8.653038
Average (Standard dev.)-0.00000044601973 (1.0000001)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions707070
Origin0.00.00.0
Limit69.069.069.0
Spacing707070
CellA=B=C: 184.8 Å
α=β=γ: 90.0 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)
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 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 65.573617 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (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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