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- PDB-6e7z: cryo-EM structure of human TRPML1 with ML-SA1 and PI35P2 -

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Basic information

Entry
Database: PDB / ID: 6e7z
Titlecryo-EM structure of human TRPML1 with ML-SA1 and PI35P2
ComponentsMucolipin-1MCOLN1
KeywordsMEMBRANE PROTEIN / human TRPML1
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 / cellular response to calcium ion / cell projection / lysosomal membrane / phagocytic vesicle membrane / late endosome / protein homotetramerization / adaptive immune response / lysosome / endosome membrane / receptor complex / lipid binding / integral component of plasma membrane / integral component of membrane / plasma membrane / cytosol / Mucolipin-1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.73 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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 27, 2018 / Release: Nov 28, 2018

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,79212
Polyers260,3404
Non-polymers4,4528
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Mucolipin-1 / MCOLN1 / ML1 / MG-2 / Mucolipidin / Transient receptor potential channel mucolipin 1 / TRPML1


Mass: 65084.996 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: MCOLN1, ML4, MSTP080 / Production host: Homo sapiens (human) / References: UniProt: Q9GZU1
#2: Chemical
ChemComp-HZ7 / (1R,2S,3S,4R,5S,6R)-5-{[(R)-[(2R)-2,3-bis{[(1S)-1-hydroxyoctyl]oxy}propoxy](hydroxy)phosphoryl]oxy}-2,4,6-trihydroxycyclohexane-1,3-diyl bis[dihydrogen (phosphate)]


Mass: 750.598 Da / Num. of mol.: 4 / Formula: C25H53O19P3
#3: Chemical
ChemComp-AQV / 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione


Mass: 362.422 Da / Num. of mol.: 4 / Formula: C22H22N2O3

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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: TRPML1MCOLN1 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: NITROGEN

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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: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameCategory
1RELIONparticle selection
4CTFFINDCTF correction
13FREALIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 45481 / Symmetry type: POINT
Least-squares processHighest resolution: 3.73 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01516021
ELECTRON MICROSCOPYf_angle_d1.15521764
ELECTRON MICROSCOPYf_dihedral_angle_d12.2259324
ELECTRON MICROSCOPYf_chiral_restr0.0572472
ELECTRON MICROSCOPYf_plane_restr0.0082660

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