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- EMDB-49382: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:... -
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Open data
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Basic information
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Title | ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG | |||||||||
![]() | ELIC5 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG | |||||||||
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![]() | ELIC / ion channel / pLGIC / Structural Protein / Membrane Protein / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Dalal V / Cheng WWL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes. Authors: Vikram Dalal / Brandon K Tan / Hanrui Xu / Wayland W L Cheng / ![]() Abstract: Detergents and lipid nanodiscs affect the cryo-EM structures of pentameric ligand-gated ion channels (pLGICs) including ELIC. To determine the structure of a pLGIC in a membrane environment that ...Detergents and lipid nanodiscs affect the cryo-EM structures of pentameric ligand-gated ion channels (pLGICs) including ELIC. To determine the structure of a pLGIC in a membrane environment that supports ion channel function, we performed single particle cryo-EM of ELIC in liposomes. ELIC activation and desensitization were confirmed in liposomes with a stopped-flow thallium flux assay. Using WT ELIC and a non-desensitizing mutant (ELIC5), we captured resting, activated and desensitized structures at high resolution. In the desensitized structure, the ion conduction pore has a constriction at the 9' leucine of the pore-lining M2 helix, indicating that 9' is the desensitization gate in ELIC. The agonist-bound structures of ELIC in liposomes are distinct from those in nanodiscs. In general, the transmembrane domain is more loosely packed in liposomes compared to nanodiscs. It has been suggested that large nanodiscs are superior for supporting membrane protein function. However, ELIC localizes to the rim of large circularized nanodiscs, and structures of ELIC in large nanodiscs deviate from the liposome structures more than those in small nanodiscs. Using liposomes for cryo-EM structure determination of a pLGIC increases our confidence that the structures are snapshots of functional states. #1: ![]() Title: Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes Authors: Dalal V / Tan BK / Xu H / Cheng WW | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.3 KB 20.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 61.1 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() ![]() | 31.3 MB 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 868 KB | Display | ![]() |
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Full document | ![]() | 867.6 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9ngcMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | ELIC5 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.868 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: ELIC5 with Propylamine facing ECD outwards in Liposomes...
File | emd_49382_additional_1.map | ||||||||||||
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Annotation | ELIC5 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ELIC5 with Propylamine facing ECD outwards in Liposomes...
File | emd_49382_half_map_1.map | ||||||||||||
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Annotation | ELIC5 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ELIC5 with Propylamine facing ECD outwards in Liposomes...
File | emd_49382_half_map_2.map | ||||||||||||
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Annotation | ELIC5 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:...
Entire | Name: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG |
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Components |
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-Supramolecule #1: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:...
Supramolecule | Name: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Erwinia chrysanthemi ligand-gated ion channel
Macromolecule | Name: Erwinia chrysanthemi ligand-gated ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 37.011055 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: APADNAADAR PVDVSVSIFI NKIYGVNTLE QTYKVDGYIV AQWTGKPRKT PGDKPLIVEN TQIERWINNG LWVPALEFIN VVGSPDTGN KRLMLFPDGR VIYNARFLGS FSNDMDFRLF PFDRQQFVLE LEPFSYNNQQ LRFSDIQVYT ENIDNEEIDE W WIRGKAST ...String: APADNAADAR PVDVSVSIFI NKIYGVNTLE QTYKVDGYIV AQWTGKPRKT PGDKPLIVEN TQIERWINNG LWVPALEFIN VVGSPDTGN KRLMLFPDGR VIYNARFLGS FSNDMDFRLF PFDRQQFVLE LEPFSYNNQQ LRFSDIQVYT ENIDNEEIDE W WIRGKAST HISDIRYDHL SSVQPNQNEF SRITVRIDAV RNPSYYLWSF ILPLGLIIAA SWSVFWLESF SERLQTSFTL ML TVVAYAF YTSNILGRLP YTTYIDQMII AGYGSIFAAI LLIIFAHHRQ ANGVEDDLLI QRSRLAFPLG FLAIGCVLVI RFF TL UniProtKB: Gamma-aminobutyric-acid receptor subunit beta-1 |
-Macromolecule #2: 3-AMINOPROPANE
Macromolecule | Name: 3-AMINOPROPANE / type: ligand / ID: 2 / Number of copies: 5 / Formula: 3CN |
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Molecular weight | Theoretical: 59.11 Da |
Chemical component information | ![]() ChemComp-3CN: |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Spherical aberration corrector: Cs Corrected System |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 56.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-9ngc: |