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Yorodumi- PDB-6c9a: Cryo-EM structure of mouse TPC1 channel in the PtdIns(3,5)P2-boun... -
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-Basic information
Entry | Database: PDB / ID: 6c9a | ||||||||||||||||||
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Title | Cryo-EM structure of mouse TPC1 channel in the PtdIns(3,5)P2-bound state | ||||||||||||||||||
Components | Two pore calcium channel protein 1 | ||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Ion channel | ||||||||||||||||||
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 / regulation of monoatomic ion transmembrane transport / phosphatidylinositol-3,5-bisphosphate binding / syntaxin binding / voltage-gated sodium channel activity ...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 / regulation of monoatomic ion transmembrane transport / phosphatidylinositol-3,5-bisphosphate binding / syntaxin binding / voltage-gated sodium channel activity / 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 / identical protein binding / membrane Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||
Authors | She, J. / Guo, J. / Chen, Q. / Bai, X. / Jiang, Y. | ||||||||||||||||||
Funding support | United States, 5items
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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 |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6c9a.cif.gz | 268.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c9a.ent.gz | 220.5 KB | Display | PDB format |
PDBx/mmJSON format | 6c9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c9a_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6c9a_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6c9a_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 6c9a_validation.cif.gz | 63.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/6c9a ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c9a | HTTPS FTP |
-Related structure data
Related structure data | 7435MC 7434C 6c96C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 95414.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tpcn1, Kiaa1169, Tpc1 / Production host: Homo sapiens (human) / References: UniProt: Q9EQJ0 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PtdIns(3,5)P2-bound mouse TPC1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293F / Plasmid: pEZT-BM |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82819 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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