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- EMDB-6823: structure of endo-lysosomal TRPML1 channel inserting into amphipo... -

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Basic information

Entry
Database: EMDB / ID: EMD-6823
Titlestructure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1
Map dataAmphipol A8-35 state 1
Sample
  • Organelle or cellular component: mammalian endo-lysosomal TRPML1 channel inserting into amphipol
    • Protein or peptide: mammalian endo-lysosomal TRPML1 channel
KeywordsmTRPML1 / mucolipidosis type IV / structual comparisons / combined regulation mechanism / MEMBRANE PROTEIN
Function / homology
Function and homology information


Transferrin endocytosis and recycling / calcium ion export / positive regulation of lysosome organization / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / phagosome maturation / NAADP-sensitive calcium-release channel activity / iron ion transmembrane transporter activity / iron ion transmembrane transport / cellular response to pH / monoatomic anion channel activity ...Transferrin endocytosis and recycling / calcium ion export / positive regulation of lysosome organization / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / phagosome maturation / NAADP-sensitive calcium-release channel activity / iron ion transmembrane transporter activity / iron ion transmembrane transport / cellular response to pH / monoatomic anion channel activity / TRP channels / sodium channel activity / endosomal transport / intracellular vesicle / monoatomic cation transmembrane transport / phagocytic cup / potassium channel activity / autophagosome maturation / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cell projection / calcium channel activity / phagocytic vesicle membrane / late endosome / late endosome membrane / protein homotetramerization / adaptive immune response / lysosome / receptor complex / lysosomal membrane / lipid binding / Golgi apparatus / nucleoplasm / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Mucolipin / : / Mucolipin, extracytosolic domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsYang M / Gao N
Funding support China, 2 items
OrganizationGrant numberCountry
the National Key R&D Program of China2017YFA0504600 and 2016YFA0501100, 2016YFA0500700 and 2017YFA0505800 China
the National Natural Science Foundation of ChinaGrant Nos. 21532004, 31570733, 31630087, and 31770936 China
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.
History
DepositionSep 15, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseDec 27, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • 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-5ydz
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_6823.png

Downloads & links

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Map

FileDownload / File: emd_6823.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAmphipol A8-35 state 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.64 Å/pix.
x 70 pix.
= 184.8 Å		2.64 Å/pix.
x 70 pix.
= 184.8 Å		2.64 Å/pix.
x 70 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 LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-12.522804000000001 - 19.836475
Average (Standard dev.)0.000000000749668 (±0.9999986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions707070
Spacing707070
CellA=B=C: 184.8 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707070
D min/max/mean-12.52319.8360.000

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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
Components
  • Organelle or cellular component: mammalian endo-lysosomal TRPML1 channel inserting into amphipol
    • Protein or peptide: mammalian endo-lysosomal TRPML1 channel

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Supramolecule #1: mammalian endo-lysosomal TRPML1 channel inserting into amphipol

SupramoleculeName: mammalian endo-lysosomal TRPML1 channel inserting into amphipol
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: mammalian endo-lysosomal TRPML1 channel

MacromoleculeName: mammalian endo-lysosomal TRPML1 channel / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 65.573617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATPAGRRAS ETERLLTPNP GYGTQVGTSP APTTPTEEED LRRRLKYFFM SPCDKFRAKG RKPCKLMLQV VKILVVTVQL ILFGLSNQL VVTFREENTI AFRHLFLLGY SDGSDDTFAA YTQEQLYQAI FYAVDQYLIL PEISLGRYAY VRGGGGPWAN G SALALCQR ...String:
MATPAGRRAS ETERLLTPNP GYGTQVGTSP APTTPTEEED LRRRLKYFFM SPCDKFRAKG RKPCKLMLQV VKILVVTVQL ILFGLSNQL VVTFREENTI AFRHLFLLGY SDGSDDTFAA YTQEQLYQAI FYAVDQYLIL PEISLGRYAY VRGGGGPWAN G SALALCQR YYHRGHVDPA NDTFDIDPRV VTDCIQVDPP DRPPDIPSED LDFLDGSASY KNLTLKFHKL INVTIHFQLK TI NLQSLIN NEIPDCYTFS ILITFDNKAH SGRIPIRLET KTHIQECKHP SVSRHGDNSF RLLFDVVVIL TCSLSFLLCA RSL LRGFLL QNEFVVFMWR RRGREISLWE RLEFVNGWYI LLVTSDVLTI SGTVMKIGIE AKNLASYDVC SILLGTSTLL VWVG VIRYL TFFHKYNILI ATLRVALPSV MRFCCCVAVI YLGYCFCGWI VLGPYHVKFR SLSMVSECLF SLINGDDMFV TFAAM QAQQ GHSSLVWLFS QLYLYSFISL FIYMVLSLFI ALITGAYDTI KHPGGTGTEK SELQAYIEQC QDSPTSGKFR RGSGSA CSL FCCCGRDSPE DHSLLVN

UniProtKB: Mucolipin-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Sugar embeddingMaterial: Amorphous ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 167000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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