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- EMDB-28832: Apo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG -

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Basic information

Entry
Database: EMDB / ID: EMD-28832
TitleApo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG
Map dataApo Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spMSP1D1
Sample
  • Complex: Apo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG
    • Protein or peptide: Erwinia chrysanthemi ligand-gated ion channel
KeywordsELIC / ion channel / pLGIC / Structural Protein / Membrane Protein / 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 / 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: 3.17 Å
AuthorsDalal V / Arcario MJ / Petroff II JT / Deitzen NM / Tan BK / Brannigan G / 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: 2024
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
DepositionNov 9, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28832.png

Downloads & links

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Map

FileDownload / File: emd_28832.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApo Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spMSP1D1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 280 pix.
= 183.96 Å		0.66 Å/pix.
x 280 pix.
= 183.96 Å		0.66 Å/pix.
x 280 pix.
= 183.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.657 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.1877377 - 0.26590326
Average (Standard dev.)0.00014681014 (±0.013888806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 183.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Apo Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spMSP1D1

Fileemd_28832_additional_1.map
AnnotationApo Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spMSP1D1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apo Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spMSP1D1

Fileemd_28832_half_map_1.map
AnnotationApo Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spMSP1D1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apo Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spMSP1D1

Fileemd_28832_half_map_2.map
AnnotationApo Wild Type ELIC in 2:1:1 POPC: POPE: POPG in spMSP1D1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG

EntireName: Apo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG
Components
  • Complex: Apo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG
    • Protein or peptide: Erwinia chrysanthemi ligand-gated ion channel

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Supramolecule #1: Apo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG

SupramoleculeName: Apo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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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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: 3000 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.332 kPa / Details: O2 27.5 sccm H2 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
Specialist opticsSpherical aberration corrector: Microscope was equipped with a Cs corrector
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 4.28 sec. / Average electron dose: 51.54 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000
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:

8d65

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36562
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8f35:
Apo ELIC in spMSP1D1 nanodiscs with 2:1:1 POPC:POPE:POPG

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