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- EMDB-41673: ELIC with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG -
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Open data
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Basic information
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Title | ELIC with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG | |||||||||
![]() | Propylamine bound Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spNW15 | |||||||||
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![]() | ELIC / ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() extracellular ligand-gated monoatomic ion channel activity / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Dalal V / Arcario MJ / Petroff II JT / Deitzen NM / Tan BK / Brannigan G / Cheng WWL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Lipid nanodisc scaffold and size alter the structure of a pentameric ligand-gated ion channel. Authors: Vikram Dalal / Mark J Arcario / John T Petroff / Brandon K Tan / Noah M Dietzen / Michael J Rau / James A J Fitzpatrick / Grace Brannigan / Wayland W L Cheng / ![]() Abstract: Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ...Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ion channel (pLGIC), Erwinia ligand-gated ion channel (ELIC), in different nanodiscs produces distinct structures by cryo-EM. The effect of the nanodisc on ELIC structure extends to the extracellular domain and agonist binding site. Additionally, molecular dynamic simulations indicate that nanodiscs of different size impact ELIC structure and that the nanodisc scaffold directly interacts with ELIC. These findings suggest that the nanodisc plays a crucial role in determining the structure of pLGICs, and that reconstitution of ion channels in larger nanodiscs may better approximate a lipid membrane environment. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 21.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.7 KB 19.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.5 KB | Display | ![]() |
Images | ![]() | 37.3 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() ![]() | 17.5 MB 17.5 MB 17.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8twzMC ![]() 8f32C ![]() 8f33C ![]() 8f34C ![]() 8f35C ![]() 8twvC C: citing same article ( M: atomic model generated by this map |
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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 | Propylamine bound Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spNW15 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.081 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Propylamine bound Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spNW15
File | emd_41673_additional_1.map | ||||||||||||
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Annotation | Propylamine bound Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spNW15 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Propylamine bound Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spNW15
File | emd_41673_half_map_1.map | ||||||||||||
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Annotation | Propylamine bound Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spNW15 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Propylamine bound Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spNW15
File | emd_41673_half_map_2.map | ||||||||||||
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Annotation | Propylamine bound Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spNW15 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ELIC with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG
Entire | Name: ELIC with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG |
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Components |
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-Supramolecule #1: ELIC with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG
Supramolecule | Name: ELIC with Propylamine in spNW15 nanodiscs 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: 36.879 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 YTSNILPRLP YTTVIDQMII AGYGSIFAAI LLIIFAHHRQ ANGVEDDLLI QRCRLAFPLG FLAIGCVLVI RGI 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: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.333 kPa / Details: O2 27.5 sccm H2 6.4 sccm Gatan Solarus |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2 seconds before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Spherical aberration corrector: Cs Corrected System |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average exposure time: 11.63 sec. / Average electron dose: 54.6 e/Å2 |
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-8twz: |