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- EMDB-43542: ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open co... -

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Basic information

Entry
Database: EMDB / ID: EMD-43542
TitleELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation
Map dataELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation
Sample
  • Complex: ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc
    • Protein or peptide: Erwinia chrysanthemi ligand-gated ion channel
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: 2-AMINO-ETHANETHIOL
KeywordsELIC / ion channel / pLGIC / TRANSPORT 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 / plasma 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
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 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)GM137957 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
DepositionJan 29, 2024-
SupersessionFeb 7, 2024ID: EMD-27220
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43542.png

Downloads & links

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Map

FileDownload / File: emd_43542.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 180 pix.
= 194.58 Å		1.08 Å/pix.
x 180 pix.
= 194.58 Å		1.08 Å/pix.
x 180 pix.
= 194.58 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.081 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.3957361 - 0.6576848
Average (Standard dev.)0.0016252826 (±0.02624422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 194.58 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in...

Fileemd_43542_additional_1.map
AnnotationELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in...

Fileemd_43542_half_map_1.map
AnnotationELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in...

Fileemd_43542_half_map_2.map
AnnotationELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation
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 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 PO...

EntireName: ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc
Components
  • Complex: ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc
    • Protein or peptide: Erwinia chrysanthemi ligand-gated ion channel
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: 2-AMINO-ETHANETHIOL

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Supramolecule #1: ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 PO...

SupramoleculeName: ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Dickeya chrysanthemi (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 chrysanthemi (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: Cys-loop ligand-gated ion channel

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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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Macromolecule #3: 2-AMINO-ETHANETHIOL

MacromoleculeName: 2-AMINO-ETHANETHIOL / type: ligand / ID: 3 / Number of copies: 5 / Formula: DHL
Molecular weightTheoretical: 77.149 Da
Chemical component information

ChemComp-DHL:
2-AMINO-ETHANETHIOL

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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 BASE (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 8 / Number real images: 1 / Average exposure time: 1.65 sec. / Average electron dose: 40.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 195134
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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