+Open data
-Basic information
Entry | Database: PDB / ID: 8atg | |||||||||
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Title | Pentameric ligand-gated ion channel GLIC with bound lipids | |||||||||
Components | Proton-gated ion channel | |||||||||
Keywords | MEMBRANE PROTEIN / GLIC / ion channel / pentameric channel / proton-gated channel | |||||||||
Function / homology | Function and homology information sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Gloeobacter violaceus (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Bergh, C. / Rovsnik, U. / Howard, R.J. / Lindahl, E. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Elife / Year: 2024 Title: Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM. Authors: Cathrine Bergh / Urška Rovšnik / Rebecca Howard / Erik Lindahl / Abstract: Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane ...Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane domain of several ion channels. However, structural details of such lipid contacts remain elusive, partly due to limited resolution of these regions in experimental structures. Here, we discovered multiple lipid interactions in the channel GLIC by integrating cryo-electron microscopy and large-scale molecular simulations. We identified 25 bound lipids in the GLIC closed state, a conformation where none, to our knowledge, were previously known. Three lipids were associated with each subunit in the inner leaflet, including a buried interaction disrupted in mutant simulations. In the outer leaflet, two intrasubunit sites were evident in both closed and open states, while a putative intersubunit site was preferred in open-state simulations. This work offers molecular details of GLIC-lipid contacts particularly in the ill-characterized closed state, testable hypotheses for state-dependent binding, and a multidisciplinary strategy for modeling protein-lipid interactions. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8atg.cif.gz | 293.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8atg.ent.gz | 240.4 KB | Display | PDB format |
PDBx/mmJSON format | 8atg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8atg_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8atg_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8atg_validation.xml.gz | 64.3 KB | Display | |
Data in CIF | 8atg_validation.cif.gz | 83.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/8atg ftp://data.pdbj.org/pub/pdb/validation_reports/at/8atg | HTTPS FTP |
-Related structure data
Related structure data | 15649MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 36291.750 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: ATCC 29082 / PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8 #2: Chemical | ChemComp-POV / ( Has ligand of interest | Y | |
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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: Pentameric ligand-gated ion channel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Gloeobacter violaceus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 25 K |
-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 / Nominal defocus max: 3600 nm / Nominal defocus min: 2200 nm |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16000 / Symmetry type: POINT | ||||||||||||||||||||||||
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