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- EMDB-0477: Cryo-EM structure of human TPC2 channel in the ligand-bound open state -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0477 | |||||||||||||||
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Title | Cryo-EM structure of human TPC2 channel in the ligand-bound open state | |||||||||||||||
![]() | Human TPC2 channel in the ligand-bound open state | |||||||||||||||
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Function / homology | ![]() endosome to lysosome transport of low-density lipoprotein particle / negative regulation of developmental pigmentation / intracellular pH reduction / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / ligand-gated sodium channel activity / NAADP-sensitive calcium-release channel activity / melanosome membrane / regulation of exocytosis / response to vitamin D / endolysosome membrane ...endosome to lysosome transport of low-density lipoprotein particle / negative regulation of developmental pigmentation / intracellular pH reduction / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / ligand-gated sodium channel activity / NAADP-sensitive calcium-release channel activity / melanosome membrane / regulation of exocytosis / response to vitamin D / endolysosome membrane / phosphatidylinositol-3,5-bisphosphate binding / monoatomic ion channel complex / lysosome organization / sodium ion transmembrane transport / smooth muscle contraction / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / monoatomic ion transmembrane transport / regulation of autophagy / calcium-mediated signaling / calcium channel activity / endocytosis involved in viral entry into host cell / Stimuli-sensing channels / intracellular calcium ion homeostasis / late endosome membrane / receptor-mediated endocytosis of virus by host cell / lysosome / endosome membrane / lysosomal membrane / protein kinase binding / identical protein binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
![]() | She J / Zeng W / Guo J / Chen Q / Bai X / Jiang Y | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mechanisms of phospholipid activation of the human TPC2 channel. Authors: Ji She / Weizhong Zeng / Jiangtao Guo / Qingfeng Chen / Xiao-Chen Bai / Youxing Jiang / ![]() ![]() Abstract: Mammalian two-pore channels (TPCs) regulate the physiological functions of the endolysosome. Here we present cryo-EM structures of human TPC2 (HsTPC2), a phosphatidylinositol 3,5-bisphosphate (PI(3,5) ...Mammalian two-pore channels (TPCs) regulate the physiological functions of the endolysosome. Here we present cryo-EM structures of human TPC2 (HsTPC2), a phosphatidylinositol 3,5-bisphosphate (PI(3,5)P)-activated, Na selective channel, in the ligand-bound and apo states. The apo structure captures the closed conformation, while the ligand-bound form features the channel in both open and closed conformations. Combined with functional analysis, these structures provide insights into the mechanism of PI(3,5)P-regulated gating of TPC2, which is distinct from that of TPC1. Specifically, the endolysosome-specific PI(3,5)P binds at the first 6-TM and activates the channel - independently of the membrane potential - by inducing a structural change at the pore-lining inner helix (IS6), which forms a continuous helix in the open state but breaks into two segments at Gly317 in the closed state. Additionally, structural comparison to the voltage-dependent TPC1 structure allowed us to identify Ile551 as being responsible for the loss of voltage dependence in TPC2. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 48.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.2 KB 11.2 KB | Display Display | ![]() |
Images | ![]() | 190.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 493.4 KB | Display | ![]() |
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Full document | ![]() | 493 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nq0MC ![]() 0478C ![]() 0479C ![]() 6nq1C ![]() 6nq2C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human TPC2 channel in the ligand-bound open state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : The complex of TPC2 with PI(3,5)P2
Entire | Name: The complex of TPC2 with PI(3,5)P2 |
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Components |
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-Supramolecule #1: The complex of TPC2 with PI(3,5)P2
Supramolecule | Name: The complex of TPC2 with PI(3,5)P2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Two pore calcium channel protein 2
Macromolecule | Name: Two pore calcium channel protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 85.671828 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GSLEMAEPQA ESEPAAGGAR GGGGDWPAGL TTYRSIQVGP GAAARWDLCI DQAVVFIEDA IQYRSINHRV DASSMWLYRR YYSNVCQRT LSFTIFLILF LAFIETPSSL TSTADVRYRA APWEPPCGLT ESVEVLCLLV FAADLSVKGY LFGWAHFQKN L WLLGYLVV ...String: GSLEMAEPQA ESEPAAGGAR GGGGDWPAGL TTYRSIQVGP GAAARWDLCI DQAVVFIEDA IQYRSINHRV DASSMWLYRR YYSNVCQRT LSFTIFLILF LAFIETPSSL TSTADVRYRA APWEPPCGLT ESVEVLCLLV FAADLSVKGY LFGWAHFQKN L WLLGYLVV LVVSLVDWTV SLSLVCHEPL RIRRLLRPFF LLQNSSMMKK TLKCIRWSLP EMASVGLLLA IHLCLFTMFG ML LFAGGKQ DDGQDRERLT YFQNLPESLT SLLVLLTTAN NPDVMIPAYS KNRAYAIFFI VFTVIGSLFL MNLLTAIIYS QFR GYLMKS LQTSLFRRRL GTRAAFEVLS SMVGEGGAFP QAVGVKPQNL LQVLQKVQLD SSHKQAMMEK VRSYGSVLLS AEEF QKLFN ELDRSVVKEH PPRPEYQSPF LQSAQFLFGH YYFDYLGNLI ALANLVSICV FLVLDADVLP AERDDFILGI LNCVF IVYY LLEMLLKVFA LGLRGYLSYP SNVFDGLLTV VLLVLEISTL AVYRLPHPGW RPEMVGLLSL WDMTRMLNML IVFRFL RII PSMKPMAVVA STVLGLVQNM RAFGGILVVV YYVFAIIGIN LFRGVIVALP GNSSLAPANG SAPCGSFEQL EYWANNF DD FAAALVTLWN LMVVNNWQVF LDAYRRYSGP WSKIYFVLWW LVSSVIWVNL FLALILENFL HKWDPRSHLQ PLAGTPEA T YQMTVELLFR DILEEPEEDE LTERLSQHPH LWLCR |
-Macromolecule #2: (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: 2 / Number of copies: 2 / Formula: EUJ |
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Molecular weight | Theoretical: 746.566 Da |
Chemical component information | ![]() ChemComp-EUJ: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33441 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |