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- EMDB-49382: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:... -

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Basic information

Entry
Database: EMDB / ID: EMD-49382
TitleELIC5 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
Map dataELIC5 with Propylamine facing ECD outwards in Liposomes with 2:1:1 POPC:POPE:POPG
Sample
  • Complex: ELIC5 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: 2.8 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
CitationJournal: 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 21, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49382.png

Downloads & links

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Map

FileDownload / File: emd_49382.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationELIC5 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.
= 222.208 Å		0.87 Å/pix.
x 256 pix.
= 222.208 Å		0.87 Å/pix.
x 256 pix.
= 222.208 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.868 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-2.5228038 - 3.6289685
Average (Standard dev.)-0.00021671566 (±0.13147682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 222.208 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: ELIC5 with Propylamine facing ECD outwards in Liposomes...

Fileemd_49382_additional_1.map
AnnotationELIC5 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: ELIC5 with Propylamine facing ECD outwards in Liposomes...

Fileemd_49382_half_map_1.map
AnnotationELIC5 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: ELIC5 with Propylamine facing ECD outwards in Liposomes...

Fileemd_49382_half_map_2.map
AnnotationELIC5 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 : ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:...

EntireName: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG
Components
  • Complex: ELIC5 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: ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:...

SupramoleculeName: ELIC5 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: 37.011055 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 YTSNILGRLP YTTYIDQMII AGYGSIFAAI LLIIFAHHRQ ANGVEDDLLI QRSRLAFPLG FLAIGCVLVI RFF 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: 2
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 electron dose: 56.9 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: 422344
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8vuw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120578
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-9ngc:
ELIC5 with propylamine facing ECD outwards in liposomes with 2:1:1 POPC:POPE:POPG

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