+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28964 | ||||||||||||
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Title | Human PAC in nanodisc at pH 4.0 with PI(4,5)P2 diC8 | ||||||||||||
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Sample |
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Function / homology | pH-gated chloride channel activity / TMEM206 protein / TMEM206 protein family / chloride transport / chloride channel complex / cell surface / plasma membrane / Proton-activated chloride channel Function and homology information | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
Authors | Ruan Z / Lu W | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Elife / Year: 2023 Title: Inhibition of the proton-activated chloride channel PAC by PIP. Authors: Ljubica Mihaljević / Zheng Ruan / James Osei-Owusu / Wei Lü / Zhaozhu Qiu / Abstract: Proton-activated chloride (PAC) channel is a ubiquitously expressed pH-sensing ion channel, encoded by (). PAC regulates endosomal acidification and macropinosome shrinkage by releasing chloride ...Proton-activated chloride (PAC) channel is a ubiquitously expressed pH-sensing ion channel, encoded by (). PAC regulates endosomal acidification and macropinosome shrinkage by releasing chloride from the organelle lumens. It is also found at the cell surface, where it is activated under pathological conditions related to acidosis and contributes to acid-induced cell death. However, the pharmacology of the PAC channel is poorly understood. Here, we report that phosphatidylinositol (4,5)-bisphosphate (PIP) potently inhibits PAC channel activity. We solved the cryo-electron microscopy structure of PAC with PIP at pH 4.0 and identified its putative binding site, which, surprisingly, locates on the extracellular side of the transmembrane domain (TMD). While the overall conformation resembles the previously resolved PAC structure in the desensitized state, the TMD undergoes remodeling upon PIP-binding. Structural and electrophysiological analyses suggest that PIP inhibits the PAC channel by stabilizing the channel in a desensitized-like conformation. Our findings identify PIP as a new pharmacological tool for the PAC channel and lay the foundation for future drug discovery targeting this channel. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28964.map.gz | 96.4 MB | EMDB map data format | |
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Header (meta data) | emd-28964-v30.xml emd-28964.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_28964.png | 126.5 KB | ||
Masks | emd_28964_msk_1.map | 103 MB | Mask map | |
Others | emd_28964_additional_1.map.gz emd_28964_half_map_1.map.gz emd_28964_half_map_2.map.gz | 51.8 MB 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28964 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28964 | HTTPS FTP |
-Validation report
Summary document | emd_28964_validation.pdf.gz | 867.6 KB | Display | EMDB validaton report |
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Full document | emd_28964_full_validation.pdf.gz | 867.1 KB | Display | |
Data in XML | emd_28964_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_28964_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28964 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28964 | HTTPS FTP |
-Related structure data
Related structure data | 8fblMC 8eq4C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28964.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28964_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_28964_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_28964_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28964_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Proton activated chloride channel at pH 4.0 with 0.5mM PIP2
Entire | Name: Proton activated chloride channel at pH 4.0 with 0.5mM PIP2 |
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Components |
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-Supramolecule #1: Proton activated chloride channel at pH 4.0 with 0.5mM PIP2
Supramolecule | Name: Proton activated chloride channel at pH 4.0 with 0.5mM PIP2 type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Proton-activated chloride channel
Macromolecule | Name: Proton-activated chloride channel / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.656955 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: FSKACLKNVF SVLLIFIYLL LMAVAVFLVY RTITDFREKL KHPVMSVSYK EVDRYDAPGI ALYPGQAQLL SCKHHYEVIP PLTSPGQPG DMNCTTQRIN YTDPFSNQTV KSALIVQGPR EVKKRELVFL QFRLNKSSED FSAIDYLLFS SFQEFLQSPN R VGFMQACE ...String: FSKACLKNVF SVLLIFIYLL LMAVAVFLVY RTITDFREKL KHPVMSVSYK EVDRYDAPGI ALYPGQAQLL SCKHHYEVIP PLTSPGQPG DMNCTTQRIN YTDPFSNQTV KSALIVQGPR EVKKRELVFL QFRLNKSSED FSAIDYLLFS SFQEFLQSPN R VGFMQACE SAYSSWKFSG GFRTWVKMSL VKTKEEDGRE AVEFRQETSV VNYIDQRPAA KKSAQLFFVV FEWKDPFIQK VQ DIVTANP WNTIALLCGA FLALFKAAEF AKLSIKWMIK IRKRYL |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #3: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...
Macromolecule | Name: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate type: ligand / ID: 3 / Number of copies: 3 / Formula: PIO |
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Molecular weight | Theoretical: 746.566 Da |
Chemical component information | ChemComp-PIO: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 24.0 µm / Nominal defocus min: 6.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84149 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |