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- EMDB-9001: cryo-EM structure of human TRPML1 with PI45P2 -

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Basic information

Entry
Database: EMDB / ID: 9001
Titlecryo-EM structure of human TRPML1 with PI45P2
Map dataprimary map
SampleTRPML1MCOLN1:
Mucolipin-1MCOLN1 / ligand
Function / homologyTransferrin endocytosis and recycling / TRP channels / Polycystin cation channel / Mucolipin / Polycystin cation channel, PKD1/PKD2 / iron ion transmembrane transporter activity / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / ligand-gated calcium channel activity / NAADP-sensitive calcium-release channel activity / cellular response to pH ...Transferrin endocytosis and recycling / TRP channels / Polycystin cation channel / Mucolipin / Polycystin cation channel, PKD1/PKD2 / iron ion transmembrane transporter activity / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / ligand-gated calcium channel activity / NAADP-sensitive calcium-release channel activity / cellular response to pH / transferrin transport / cation channel activity / cation transport / phagocytic cup / autophagosome maturation / late endosome membrane / calcium channel activity / calcium ion transmembrane transport / cell projection / cellular response to calcium ion / lysosomal membrane / phagocytic vesicle membrane / late endosome / protein homotetramerization / adaptive immune response / lysosome / receptor complex / endosome membrane / lipid binding / integral component of plasma membrane / integral component of membrane / plasma membrane / cytosol / Mucolipin-1
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.57 Å resolution
AuthorsSchmiege P / Li X
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for PtdInsP-mediated human TRPML1 regulation.
Authors: Michael Fine / Philip Schmiege / Xiaochun Li
Validation ReportPDB-ID: 6e7y

SummaryFull reportAbout validation report
DateDeposition: Jul 27, 2018 / Header (metadata) release: Oct 31, 2018 / Map release: Nov 28, 2018 / Last update: Nov 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.68
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.68
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6e7y
  • Surface level: 3.68
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9001.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.07 Å/pix.
= 321. Å
300 pix
1.07 Å/pix.
= 321. Å
300 pix
1.07 Å/pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:3.68 (by author), 3.68 (movie #1):
Minimum - Maximum-8.451521 - 15.191998999999999
Average (Standard dev.)-0.043590937 (0.45675966)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z321.000321.000321.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-8.45215.192-0.044

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Supplemental data

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Sample components

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Entire TRPML1

EntireName: TRPML1 / Number of components: 3

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Component #1: protein, TRPML1

ProteinName: TRPML1MCOLN1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Mucolipin-1

ProteinName: Mucolipin-1MCOLN1 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 65.084996 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,...

LigandName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.746566 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 7 mg/ml / pH: 7
Support filmunspecified
VitrificationCryogen name: NITROGEN

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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: 1.6 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: 69587
3D reconstructionSoftware: FREALIX / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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