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- EMDB-49390: ELIC state 1 with propylamine facing ECD outwards in liposomes wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-49390
TitleELIC state 1 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
Map dataWild Type ELIC state 1 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG
Sample
  • Complex: ELIC state 1 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
    • Protein or peptide: Erwinia chrysanthemi ligand-gated ion channel
  • Ligand: 3-AMINOPROPANE
  • Ligand: SODIUM ION
KeywordsELIC / ion channel / pLGIC / Structural Protein / Membrane Protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDalal V / Cheng WWL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137957 United States
American Heart Association24POST1189869 United States
Citation
Journal: Elife / Year: 2025
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: Journal: Elife / Year: 2025
Title: Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes
Authors: Dalal V / Tan BK / Xu H / Cheng WW
History
DepositionFeb 22, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49390.png

Downloads & links

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Map

FileDownload / File: emd_49390.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWild Type ELIC state 1 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 221.44 Å		0.87 Å/pix.
x 256 pix.
= 221.44 Å		0.87 Å/pix.
x 256 pix.
= 221.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.865 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.07757514 - 0.10718411
Average (Standard dev.)0.000011309611 (±0.004469529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 221.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Wild Type ELIC state 1 with Propylamine facing...

Fileemd_49390_additional_1.map
AnnotationWild Type ELIC state 1 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Wild Type ELIC state 1 with Propylamine facing...

Fileemd_49390_half_map_1.map
AnnotationWild Type ELIC state 1 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Wild Type ELIC state 1 with Propylamine facing...

Fileemd_49390_half_map_2.map
AnnotationWild Type ELIC state 1 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ELIC state 1 with propylamine facing ECD outwards in liposomes wi...

EntireName: ELIC state 1 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
Components
  • Complex: ELIC state 1 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
    • Protein or peptide: Erwinia chrysanthemi ligand-gated ion channel
  • Ligand: 3-AMINOPROPANE
  • Ligand: SODIUM ION

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Supramolecule #1: ELIC state 1 with propylamine facing ECD outwards in liposomes wi...

SupramoleculeName: ELIC state 1 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Dickeya dadantii (bacteria)

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Macromolecule #1: Erwinia chrysanthemi ligand-gated ion channel

MacromoleculeName: Erwinia chrysanthemi ligand-gated ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Dickeya dadantii (bacteria)
Molecular weightTheoretical: 36.879 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: 3-AMINOPROPANE

MacromoleculeName: 3-AMINOPROPANE / type: ligand / ID: 2 / Number of copies: 5 / Formula: 3CN
Molecular weightTheoretical: 59.11 Da
Chemical component information

ChemComp-3CN:
3-AMINOPROPANE

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 6
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Cs Corrected System
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average exposure time: 7.27 sec. / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen 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

Particle selectionNumber selected: 635388
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8f34

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15718
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9ngq:
ELIC state 1 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG

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