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- EMDB-27217: ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-27217
TitleELIC apo in 2:1:1 POPC:POPE:POPG nanodisc
Map data
Sample
  • Complex: ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc
    • Protein or peptide: Erwinia ligand-gated ion channel
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
KeywordsELIC / 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 / 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: 3.47 Å
AuthorsPetroff II JT / Deng Z / Rau MJ / Fitzpatrick JAJ / Yuan P / Cheng WWL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM137957 United States
CitationJournal: 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
DepositionJun 6, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27217.png

Downloads & links

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Map

FileDownload / File: emd_27217.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 180 pix.
= 198. Å		1.1 Å/pix.
x 180 pix.
= 198. Å		1.1 Å/pix.
x 180 pix.
= 198. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0264
Minimum - Maximum-0.13831432 - 0.21939537
Average (Standard dev.)0.00004442667 (±0.009126394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 198.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_27217_additional_1.map
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Half map: #2

Fileemd_27217_half_map_1.map
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Half map: #1

Fileemd_27217_half_map_2.map
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Sample components

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Entire : ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc

EntireName: ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc
Components
  • Complex: ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc
    • Protein or peptide: Erwinia ligand-gated ion channel
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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Supramolecule #1: ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc

SupramoleculeName: ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Dickeya dadantii (bacteria)

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Macromolecule #1: Erwinia ligand-gated ion channel

MacromoleculeName: Erwinia 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: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

MacromoleculeName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 2 / Number of copies: 5 / Formula: PGW
Molecular weightTheoretical: 749.007 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: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.332 kPa / Details: H2 27.5 sccm O2 6.4 sccm
VitrificationCryogen 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

MicroscopeFEI TITAN KRIOS
TemperatureMin: 82.0 K / Max: 84.0 K
Specialist opticsSpherical aberration corrector: Microscope was equipped with a Cs corrector
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2yn6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165015
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2yn6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8d65:
ELIC apo in 2:1:1 POPC:POPE:POPG nanodisc

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