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- EMDB-20968: ELIC-propylammonium complex in POPC-only nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-20968
TitleELIC-propylammonium complex in POPC-only nanodiscs
Map dataELIC-propylammonium complex in POPC-only nanodiscs
Sample
  • Complex: ELIC-propylammonium complex in POPC-only nanodiscs.
    • Protein or peptide: Gamma-aminobutyric-acid receptor subunit beta-1
  • Ligand: 3-AMINOPROPANE
KeywordsPentameric Ligand-gated Ion Channels / POPC / Propylamonium / Nanodisc / Cys-loop receptor / MEMBRANE 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 3937 (bacteria) / Dickeya dadantii (strain 3937) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGrosman C / Kumar P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)NS042169 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS042169 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer.
Authors: Pramod Kumar / Yuhang Wang / Zhening Zhang / Zhiyu Zhao / Gisela D Cymes / Emad Tajkhorshid / Claudio Grosman /
Abstract: The lipid dependence of the nicotinic acetylcholine receptor from the electric organ has long been recognized, and one of the most consistent experimental observations is that, when reconstituted in ...The lipid dependence of the nicotinic acetylcholine receptor from the electric organ has long been recognized, and one of the most consistent experimental observations is that, when reconstituted in membranes formed by zwitterionic phospholipids alone, exposure to agonist fails to elicit ion-flux activity. More recently, it has been suggested that the bacterial homolog ELIC ( ligand-gated ion channel) has a similar lipid sensitivity. As a first step toward the elucidation of the structural basis of this phenomenon, we solved the structures of ELIC embedded in palmitoyl-oleoyl-phosphatidylcholine- (POPC-) only nanodiscs in both the unliganded (4.1-Å resolution) and agonist-bound (3.3 Å) states using single-particle cryoelectron microscopy. Comparison of the two structural models revealed that the largest differences occur at the level of loop C-at the agonist-binding sites-and the loops at the interface between the extracellular and transmembrane domains (ECD and TMD, respectively). On the other hand, the transmembrane pore is occluded in a remarkably similar manner in both structures. A straightforward interpretation of these findings is that POPC-only membranes frustrate the ECD-TMD coupling in such a way that the "conformational wave" of liganded-receptor gating takes place in the ECD and the interfacial M2-M3 linker but fails to penetrate the membrane and propagate into the TMD. Furthermore, analysis of the structural models and molecular simulations suggested that the higher affinity for agonists characteristic of the open- and desensitized-channel conformations results, at least in part, from the tighter confinement of the ligand to its binding site; this limits the ligand's fluctuations, and thus delays its escape into bulk solvent.
History
DepositionNov 18, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseJan 15, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v03
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_20968.png

Downloads & links

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Map

FileDownload / File: emd_20968.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationELIC-propylammonium complex in POPC-only nanodiscs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 219.22 Å		1.1 Å/pix.
x 200 pix.
= 219.22 Å		1.1 Å/pix.
x 200 pix.
= 219.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0961 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.07
Minimum - Maximum-0.36151645 - 0.64890957
Average (Standard dev.)0.0012879248 (±0.018875193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 219.22 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09611.09611.0961
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z219.220219.220219.220
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.3620.6490.001

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Supplemental data

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Half map: ELIC-propylammonium complex in POPC-only nanodiscs

Fileemd_20968_half_map_1.map
AnnotationELIC-propylammonium complex in POPC-only nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ELIC-propylammonium complex in POPC-only nanodiscs

Fileemd_20968_half_map_2.map
AnnotationELIC-propylammonium complex in POPC-only nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ELIC-propylammonium complex in POPC-only nanodiscs.

EntireName: ELIC-propylammonium complex in POPC-only nanodiscs.
Components
  • Complex: ELIC-propylammonium complex in POPC-only nanodiscs.
    • Protein or peptide: Gamma-aminobutyric-acid receptor subunit beta-1
  • Ligand: 3-AMINOPROPANE

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Supramolecule #1: ELIC-propylammonium complex in POPC-only nanodiscs.

SupramoleculeName: ELIC-propylammonium complex in POPC-only nanodiscs. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Dickeya dadantii 3937 (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 (strain 3937) (bacteria) / Strain: 3937
Molecular weightTheoretical: 36.664742 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

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: 10 / 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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMNa2HPO4Sodium phospate buffer
NaH2PO4Sodium phospate buffer
150.0 mMNaClSodium Chloride

Details: 150 NaCl and 10 sodium phosphate, pH 8.0.
GridModel: Homemade / Material: GOLD
VitrificationCryogen name: ETHANE / Instrument: SPOTITON

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: COUNTING / Average electron dose: 63.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 667903
Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 98696
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6v03:
ELIC-propylammonium complex in POPC-only nanodiscs

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