[English] 日本語
Yorodumi- EMDB-7435: Cryo-EM structure of mouse TPC1 channel in the PtdIns(3,5)P2-boun... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7435 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of mouse TPC1 channel in the PtdIns(3,5)P2-bound state | ||||||||||||||||||
Map data | TPC1 channel in the PtdIns(3,5)P2-bound state | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Function / homology | Function and homology information endolysosome / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / ligand-gated sodium channel activity / NAADP-sensitive calcium-release channel activity / voltage-gated monoatomic ion channel activity / Stimuli-sensing channels / voltage-gated sodium channel activity / regulation of monoatomic ion transmembrane transport / phosphatidylinositol-3,5-bisphosphate binding / syntaxin binding ...endolysosome / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / ligand-gated sodium channel activity / NAADP-sensitive calcium-release channel activity / voltage-gated monoatomic ion channel activity / Stimuli-sensing channels / voltage-gated sodium channel activity / regulation of monoatomic ion transmembrane transport / phosphatidylinositol-3,5-bisphosphate binding / syntaxin binding / sodium ion transmembrane transport / positive regulation of autophagy / endocytosis involved in viral entry into host cell / recycling endosome membrane / early endosome membrane / endosome membrane / lysosomal membrane / protein homodimerization activity / membrane / identical protein binding Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||
Authors | She J / Guo J / Chen Q / Bai X / Jiang Y | ||||||||||||||||||
Funding support | United States, 5 items
| ||||||||||||||||||
Citation | Journal: Nature / Year: 2018 Title: Structural insights into the voltage and phospholipid activation of the mammalian TPC1 channel. Authors: Ji She / Jiangtao Guo / Qingfeng Chen / Weizhong Zeng / Youxing Jiang / Xiao-Chen Bai / Abstract: The organellar two-pore channel (TPC) functions as a homodimer, in which each subunit contains two homologous Shaker-like six-transmembrane (6-TM)-domain repeats. TPCs belong to the voltage-gated ion ...The organellar two-pore channel (TPC) functions as a homodimer, in which each subunit contains two homologous Shaker-like six-transmembrane (6-TM)-domain repeats. TPCs belong to the voltage-gated ion channel superfamily and are ubiquitously expressed in animals and plants. Mammalian TPC1 and TPC2 are localized at the endolysosomal membrane, and have critical roles in regulating the physiological functions of these acidic organelles. Here we present electron cryo-microscopy structures of mouse TPC1 (MmTPC1)-a voltage-dependent, phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P)-activated Na-selective channel-in both the apo closed state and ligand-bound open state. Combined with functional analysis, these structures provide comprehensive structural insights into the selectivity and gating mechanisms of mammalian TPC channels. The channel has a coin-slot-shaped ion pathway in the filter that defines the selectivity of mammalian TPCs. Only the voltage-sensing domain from the second 6-TM domain confers voltage dependence on MmTPC1. Endolysosome-specific PtdIns(3,5)P binds to the first 6-TM domain and activates the channel under conditions of depolarizing membrane potential. Structural comparisons between the apo and PtdIns(3,5)P-bound structures show the interplay between voltage and ligand in channel activation. These MmTPC1 structures reveal lipid binding and regulation in a 6-TM voltage-gated channel, which is of interest in light of the emerging recognition of the importance of phosphoinositide regulation of ion channels. | ||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7435.map.gz | 48.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-7435-v30.xml emd-7435.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_7435.png | 94.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7435 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7435 | HTTPS FTP |
-Related structure data
Related structure data | 6c9aMC 7434C 6c96C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_7435.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TPC1 channel in the PtdIns(3,5)P2-bound state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : PtdIns(3,5)P2-bound mouse TPC1
Entire | Name: PtdIns(3,5)P2-bound mouse TPC1 |
---|---|
Components |
|
-Supramolecule #1: PtdIns(3,5)P2-bound mouse TPC1
Supramolecule | Name: PtdIns(3,5)P2-bound mouse TPC1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pEZT-BM |
-Macromolecule #1: Two pore calcium channel protein 1
Macromolecule | Name: Two pore calcium channel protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 95.414758 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAVSLDDDVP LILTLDEAES APLPPSNSLG QEQLPSKNGG SHSIHNSQVP SLVSGADSPP SSPTGHNWEM NYQEAAIYLQ EGQNNDKFF THPKDARALA AYLFVHNHFF YMMELLTALL LLLLSLCESP AVPVLKLHTY VHATLELFAL MVVVFELCMK L RWLGFHTF ...String: MAVSLDDDVP LILTLDEAES APLPPSNSLG QEQLPSKNGG SHSIHNSQVP SLVSGADSPP SSPTGHNWEM NYQEAAIYLQ EGQNNDKFF THPKDARALA AYLFVHNHFF YMMELLTALL LLLLSLCESP AVPVLKLHTY VHATLELFAL MVVVFELCMK L RWLGFHTF VRHKRTMVKT SVLVVQFIEA IVVLVRQTSH VRVTRALRCI FLVDCRYCGG VRRNLRQIFQ SLPPFMDILL LL LFFMIIF AILGFYLFST NPSDPYFSTL ENSIVNLFVL LTTANFPDVM MPSYSRNPWS CVFFIVYLSI ELYFIMNLLL AVV FDTFND IEKHKFKSLL LHKRTAIQHA YGLLASQRRP AGISYRQFEG LMRFYKPRMS ARERFLTFKA LNQSNTPLLS LKDF YDIYE VAALQWKAKR NRQHWFDELP RTAFLIFKGI NILVNSKAFQ YFMYLVVAVN GVWILVETFM LKGGNFTSKH VPWSY LVFL TIYGVELFMK VAGLGPVEYL SSGWNLFDFS VTAFAFLGLL ALTLNMEPFY FIVVLRPLQL LRLFKLKKRY RNVLDT MFE LLPRMASLGL TLLTFYYSFA IVGMEFFNGR LTPNCCNTST VADAYRFINH TVGNKTKVEE GYYYLNNFDN ILNSFVT LF ELTVVNNWYI IMEGVTSQTS HWSRLYFMTF YIVTMVVMTI IVAFILEAFV FRMNYSRKSQ DSEVDSGIVI EKEMSKEE L MAVLELYREE RGTSSDVTRL LDTLSQMEKY QQNSMVFLGR RSRTKSDLSL KMYQEEIQEW YEEHAREQEQ QKLRGSVPG PAAQQPPGSR QRSQTVTVEA GLVPR |
-Macromolecule #3: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bi...
Macromolecule | Name: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate type: ligand / ID: 3 / Number of copies: 2 / Formula: EUJ |
---|---|
Molecular weight | Theoretical: 746.566 Da |
Chemical component information | ChemComp-EUJ: |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82819 |