+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27216 | |||||||||
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Title | ELIC with cysteamine in POPC nanodisc | |||||||||
Map data | Sharpened map of WT ELIC in POPC within an MSP1E3D1 scaffold. | |||||||||
Sample |
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Keywords | ELIC / ion channel / pLGIC / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Dickeya dadantii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||
Authors | Petroff II JT / Deng Z / Rau MJ / Fitzpatrick JAJ / Yuan P / Cheng WWL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27216.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-27216-v30.xml emd-27216.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27216_fsc.xml | 6.4 KB | Display | FSC data file |
Images | emd_27216.png | 92.5 KB | ||
Filedesc metadata | emd-27216.cif.gz | 6.3 KB | ||
Others | emd_27216_additional_1.map.gz emd_27216_half_map_1.map.gz emd_27216_half_map_2.map.gz | 16.8 MB 16.9 MB 16.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27216 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27216 | HTTPS FTP |
-Related structure data
Related structure data | 8d64MC 8d63C 8d65C 8d66C 8d67C 8vuwC 27220 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27216.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map of WT ELIC in POPC within an MSP1E3D1 scaffold. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map of WT ELIC in POPC within an MSP1E3D1 scaffold.
File | emd_27216_additional_1.map | ||||||||||||
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Annotation | Unsharpened map of WT ELIC in POPC within an MSP1E3D1 scaffold. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unsharpened half map 1 of WT ELIC in...
File | emd_27216_half_map_1.map | ||||||||||||
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Annotation | Unsharpened half map 1 of WT ELIC in POPC within an MSP1E3D1 scaffold. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unsharpened half map 2 of WT ELIC in...
File | emd_27216_half_map_2.map | ||||||||||||
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Annotation | Unsharpened half map 2 of WT ELIC in POPC within an MSP1E3D1 scaffold. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ELIC with cysteamine in POPC nanodisc
Entire | Name: ELIC with cysteamine in POPC nanodisc |
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Components |
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-Supramolecule #1: ELIC with cysteamine in POPC nanodisc
Supramolecule | Name: ELIC with cysteamine in POPC nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Dickeya dadantii (bacteria) |
-Macromolecule #1: Erwinia ligand-gated ion channel
Macromolecule | Name: Erwinia ligand-gated ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Dickeya dadantii (bacteria) |
Molecular weight | Theoretical: 35.383367 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PVDVSVSIFI NKIYGVNTLE QTYKVDGYIV AQWTGKPRKT PGDKPLIVEN TQIERWINNG LWVPALEFIN VVGSPDTGNK RLMLFPDGR VIYNARFLGS FSNDMDFRLF PFDRQQFVLE LEPFSYNNQQ LRFSDIQVYT ENIDNEEIDE WWIRGKASTH I SDIRYDHL ...String: PVDVSVSIFI NKIYGVNTLE QTYKVDGYIV AQWTGKPRKT PGDKPLIVEN TQIERWINNG LWVPALEFIN VVGSPDTGNK RLMLFPDGR VIYNARFLGS FSNDMDFRLF PFDRQQFVLE LEPFSYNNQQ LRFSDIQVYT ENIDNEEIDE WWIRGKASTH I SDIRYDHL SSVQPNQNEF SRITVRIDAV RNPSYYLWSF ILPLGLIIAA SWSVFWLESF SERLQTSFTL MLTVVAYAFY TS NILPRLP YTTVIDQMII AGYGSIFAAI LLIIFAHHRQ ANGVEDDLLI QRCRLAFPLG FLAIGCVLVI UniProtKB: Gamma-aminobutyric-acid receptor subunit beta-1 |
-Macromolecule #2: 2-AMINO-ETHANETHIOL
Macromolecule | Name: 2-AMINO-ETHANETHIOL / type: ligand / ID: 2 / Number of copies: 5 / Formula: DHL |
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Molecular weight | Theoretical: 77.149 Da |
Chemical component information | ChemComp-DHL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.332 kPa / Details: O2 27.5 sccm H2 6.4 sccm |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 150.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Specialist optics | Spherical aberration corrector: Microscope was equipped with a Cs corrector Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 82.0 K / Max: 84.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Average exposure time: 8.0 sec. / Average electron dose: 1.65 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |