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- EMDB-41672: ELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG -

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Basic information

Entry
Database: EMDB / ID: EMD-41672
TitleELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG
Map data
Sample
  • Complex: ELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG
    • Protein or peptide: Gamma-aminobutyric-acid receptor subunit beta-1
  • Ligand: 3-AMINOPROPANE
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: 3.4 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
DepositionAug 21, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41672.png

Downloads & links

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Map

FileDownload / File: emd_41672.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 180 pix.
= 213.12 Å		1.18 Å/pix.
x 180 pix.
= 213.12 Å		1.18 Å/pix.
x 180 pix.
= 213.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.184 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.67
Minimum - Maximum-3.1998541 - 5.5922513
Average (Standard dev.)0.008819546 (±0.22003111)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 213.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_41672_additional_1.map
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Half map: #2

Fileemd_41672_half_map_1.map
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Half map: #1

Fileemd_41672_half_map_2.map
Projections & Slices
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Sample components

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Entire : ELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG

EntireName: ELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG
Components
  • Complex: ELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG
    • Protein or peptide: Gamma-aminobutyric-acid receptor subunit beta-1
  • Ligand: 3-AMINOPROPANE

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Supramolecule #1: ELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG

SupramoleculeName: ELIC5 with Propylamine in spNW15 nanodiscs 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: Gamma-aminobutyric-acid receptor subunit beta-1

MacromoleculeName: Gamma-aminobutyric-acid receptor subunit beta-1 / 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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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: 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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average exposure time: 11.78 sec. / Average electron dose: 50.09 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 120000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

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

8d68
PDB Unreleased entry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27201
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-8twv:
ELIC5 with Propylamine in spNW15 nanodiscs with 2:1:1 POPC:POPE:POPG

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