+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0478 | |||||||||||||||
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Title | Cryo-EM structure of human TPC2 channel in the apo state | |||||||||||||||
Map data | Human TPC2 channel in the apo state | |||||||||||||||
Sample |
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Function / homology | Function and homology information 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 / regulation of exocytosis / melanosome membrane / endolysosome membrane / response to vitamin D ...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 / regulation of exocytosis / melanosome membrane / endolysosome membrane / response to vitamin D / phosphatidylinositol-3,5-bisphosphate binding / monoatomic ion channel complex / lysosome organization / smooth muscle contraction / voltage-gated calcium channel activity / sodium ion transmembrane transport / release of sequestered calcium ion into cytosol / regulation of autophagy / calcium-mediated signaling / calcium channel activity / endocytosis involved in viral entry into host cell / Stimuli-sensing channels / intracellular calcium ion homeostasis / monoatomic ion transmembrane transport / 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 | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | She J / Zeng W / Guo J / Chen Q / Bai X / Jiang Y | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Elife / Year: 2019 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0478.map.gz | 48.6 MB | EMDB map data format | |
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Header (meta data) | emd-0478-v30.xml emd-0478.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_0478.png | 187 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0478 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0478 | HTTPS FTP |
-Validation report
Summary document | emd_0478_validation.pdf.gz | 492.4 KB | Display | EMDB validaton report |
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Full document | emd_0478_full_validation.pdf.gz | 492 KB | Display | |
Data in XML | emd_0478_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_0478_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0478 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0478 | HTTPS FTP |
-Related structure data
Related structure data | 6nq1MC 0477C 0479C 6nq0C 6nq2C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0478.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human TPC2 channel in the apo state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Two-pore channel 2
Entire | Name: Two-pore channel 2 |
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Components |
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-Supramolecule #1: Two-pore channel 2
Supramolecule | Name: Two-pore channel 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 85.671828 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96361 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |