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Yorodumi- EMDB-8883: Cryo-EM structure of mammalian endolysosomal TRPML1 channel in na... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8883 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs at 3.59 Angstrom resolution | ||||||||||||||||||||||||
Map data | Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs at 3.59 Angstrom resolution | ||||||||||||||||||||||||
Sample |
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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 / NAADP-sensitive calcium-release channel activity / phagosome maturation / cellular response to pH / ligand-gated calcium channel activity / TRP channels / endosomal transport ...Transferrin endocytosis and recycling / calcium ion export / positive regulation of lysosome organization / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / NAADP-sensitive calcium-release channel activity / phagosome maturation / cellular response to pH / ligand-gated calcium channel activity / TRP channels / endosomal transport / phagocytic cup / intracellular vesicle / autophagosome maturation / monoatomic cation transmembrane transport / localization / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cell projection / calcium ion transmembrane transport / phagocytic vesicle membrane / late endosome / late endosome membrane / protein homotetramerization / adaptive immune response / lysosome / receptor complex / lysosomal membrane / intracellular membrane-bounded organelle / lipid binding / Golgi apparatus / nucleoplasm / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | ||||||||||||||||||||||||
Authors | Chen Q / She J / Guo J / Bai X / Jiang Y | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: Nature / Year: 2017 Title: Structure of mammalian endolysosomal TRPML1 channel in nanodiscs. Authors: Qingfeng Chen / Ji She / Weizhong Zeng / Jiangtao Guo / Haoxing Xu / Xiao-Chen Bai / Youxing Jiang / Abstract: Transient receptor potential mucolipin 1 (TRPML1) is a cation channel located within endosomal and lysosomal membranes. Ubiquitously expressed in mammalian cells, its loss-of-function mutations are ...Transient receptor potential mucolipin 1 (TRPML1) is a cation channel located within endosomal and lysosomal membranes. Ubiquitously expressed in mammalian cells, its loss-of-function mutations are the direct cause of type IV mucolipidosis, an autosomal recessive lysosomal storage disease. Here we present the single-particle electron cryo-microscopy structure of the mouse TRPML1 channel embedded in nanodiscs. Combined with mutagenesis analysis, the TRPML1 structure reveals that phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P) binds to the N terminus of the channel-distal from the pore-and the helix-turn-helix extension between segments S2 and S3 probably couples ligand binding to pore opening. The tightly packed selectivity filter contains multiple ion-binding sites, and the conserved acidic residues form the luminal Ca-blocking site that confers luminal pH and Ca modulation on channel conductance. A luminal linker domain forms a fenestrated canopy atop the channel, providing several luminal ion passages to the pore and creating a negative electrostatic trap, with a preference for divalent cations, at the luminal entrance. The structure also reveals two equally distributed S4-S5 linker conformations in the closed channel, suggesting an S4-S5 linker-mediated PtdInsP gating mechanism among TRPML channels. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8883.map.gz | 27.2 MB | EMDB map data format | |
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Header (meta data) | emd-8883-v30.xml emd-8883.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_8883.png | 239.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8883 | HTTPS FTP |
-Related structure data
Related structure data | 5wpvMC 8881C 8882C 5wpqC 5wptC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8883.map.gz / Format: CCP4 / Size: 29.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs at 3.59 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Homotetramer of mouse TRPML1
Entire | Name: Homotetramer of mouse TRPML1 |
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Components |
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-Supramolecule #1: Homotetramer of mouse TRPML1
Supramolecule | Name: Homotetramer of mouse TRPML1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 66 KDa |
-Macromolecule #1: Mucolipin-1
Macromolecule | Name: Mucolipin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 66.656812 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 DHSLLVNVDG GSSGGLVPR |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.3 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 150.0 mM / Component - Formula: NaClSodium chloride / Component - Name: sodium chloride Details: Solutions were made fresh from stock solutions and filtered. |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 46730 |
Specialist optics | Energy filter - Name: GIFQuantum / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3000 / Average exposure time: 15.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1433949 / Details: The particles were auto-picked in RELION. |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: OTHER / Software - Name: RELION (ver. 2) / Details: The initial model is from a model of TRPV1. |
Final 3D classification | Number classes: 8 / Software - Name: RELION (ver. 2) Details: We did the focus classification with density subtraction for the TM domain with RELION. |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2) Details: Auto-refinement in RELION generated the final reconstruction. The angular sampling was determined automatically in RELION. |
Final reconstruction | Number classes used: 5 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 20000 |
Details | 30 frames per movie stack were saved for motion correction. |