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- EMDB-7019: TRPML3/ML-SA1 complex at pH 7.4 -

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Basic information

Entry
Database: EMDB / ID: 7019
TitleTRPML3/ML-SA1 complex at pH 7.4
Map data
SampleTRPML3 channel bound with a agonist ML-SA1:
Mucolipin-3 / ligand
Function / homologyMucolipin / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / TRP channels / inner ear auditory receptor cell differentiation / autophagosome membrane / calcium channel activity / late endosome membrane / calcium ion transmembrane transport / locomotory behavior ...Mucolipin / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / TRP channels / inner ear auditory receptor cell differentiation / autophagosome membrane / calcium channel activity / late endosome membrane / calcium ion transmembrane transport / locomotory behavior / lysosomal membrane / early endosome membrane / lipid binding / integral component of membrane / plasma membrane / Mucolipin-3
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.62 Å resolution
AuthorsZhou X / Li M
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states.
Authors: Xiaoyuan Zhou / Minghui Li / Deyuan Su / Qi Jia / Huan Li / Xueming Li / Jian Yang
Validation ReportPDB-ID: 6ayf

SummaryFull reportAbout validation report
DateDeposition: Sep 8, 2017 / Header (metadata) release: Oct 18, 2017 / Map release: Nov 8, 2017 / Last update: Dec 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.293
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.293
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6ayf
  • Surface level: 0.293
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7019.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.34 Å/pix.
= 214.08 Å
160 pix
1.34 Å/pix.
= 214.08 Å
160 pix
1.34 Å/pix.
= 214.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.338 Å
Density
Contour Level:0.293 (by author), 0.293 (movie #1):
Minimum - Maximum-1.3926152 - 1.8566403
Average (Standard dev.)0.0076051643 (0.07017273)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
CellA=B=C: 214.08002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z214.080214.080214.080
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-1.3931.8570.008

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Supplemental data

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Sample components

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Entire TRPML3 channel bound with a agonist ML-SA1

EntireName: TRPML3 channel bound with a agonist ML-SA1 / Number of components: 3

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Component #1: protein, TRPML3 channel bound with a agonist ML-SA1

ProteinName: TRPML3 channel bound with a agonist ML-SA1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Mucolipin-3

ProteinName: Mucolipin-3 / Recombinant expression: No
MassTheoretical: 64.625785 kDa
Source (engineered)Expression System: Homo sapiens (human) / Vector: pFastbac1

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.9 mg/ml / Buffer solution: ML-SA1 was added before sample was frozen. / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 100 %

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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: SPOT SCAN
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 50726
3D reconstructionSoftware: THUNDER / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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