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Open data
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Basic information
Entry | Database: PDB / ID: 8d65 | ||||||
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Title | ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc | ||||||
![]() | Erwinia ligand-gated ion channel | ||||||
![]() | STRUCTURAL PROTEIN / ELIC / ion channel / pLGIC | ||||||
Function / homology | ![]() extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å | ||||||
![]() | Petroff II, J.T. / Deng, Z. / Rau, M.J. / Fitzpatrick, J.A.J. / Yuan, P. / Cheng, W.W.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Authors: John T Petroff / Noah M Dietzen / Ezry Santiago-McRae / Brett Deng / Maya S Washington / Lawrence J Chen / K Trent Moreland / Zengqin Deng / Michael Rau / James A J Fitzpatrick / Peng Yuan / ...Authors: John T Petroff / Noah M Dietzen / Ezry Santiago-McRae / Brett Deng / Maya S Washington / Lawrence J Chen / K Trent Moreland / Zengqin Deng / Michael Rau / James A J Fitzpatrick / Peng Yuan / Thomas T Joseph / Jérôme Hénin / Grace Brannigan / Wayland W L Cheng / ![]() ![]() Abstract: Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. ...Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.4 KB | Display | ![]() |
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PDB format | ![]() | 231.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 27217MC ![]() 8d63C ![]() 8d64C ![]() 8d66C ![]() 8d67C ![]() 8vuwC ![]() 27220 M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 36879.000 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PGW / ( 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 |
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Sample preparation
Component | Name: ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: H2 27.5 sccm O2 6.4 sccm / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot for 2 seconds before plunging |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 0.01 mm / C2 aperture diameter: 150 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 84 K / Temperature (min): 82 K |
Image recording | Average exposure time: 8 sec. / Electron dose: 1.65 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV Spherical aberration corrector: Microscope was equipped with a Cs corrector |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 |
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Processing
EM software | Name: EPU / Version: 2.9.0.1519 / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165015 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |
Atomic model building | PDB-ID: 2YN6 Accession code: 2YN6 / Source name: PDB / Type: experimental model |