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- EMDB-20489: Human alpha3beta4 nicotinic acetylcholine receptor in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-20489
TitleHuman alpha3beta4 nicotinic acetylcholine receptor in complex with nicotine in saposin nanodiscs without CHS
Map data
Sample
  • Complex: Human alpha3beta4 nicotinic receptor in complex with Fab fragments and bound to nicotine
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsGharpure A / Teng J / Zhuang Y / Noviello CM / Walsh RM / Cabuco R / Howard RJ / Zaveri NT / Lindahl E / Hibbs RE
Funding support United States, 6 items
OrganizationGrant numberCountry
Welch FoundationI-1812 United States
National Institutes of Health/National Institute on Drug AbuseT32DA07290 United States
National Institutes of Health/National Institute of General Medical SciencesT32GM008203 United States
National Institutes of Health/National Institute on Drug AbuseDA037492 United States
National Institutes of Health/National Institute on Drug AbuseDA042072 United States
National Institutes of Health/National Institute of Neurological Disorders and StrokeNS095899 United States
CitationJournal: Neuron / Year: 2019
Title: Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic Receptor.
Authors: Anant Gharpure / Jinfeng Teng / Yuxuan Zhuang / Colleen M Noviello / Richard M Walsh / Rico Cabuco / Rebecca J Howard / Nurulain T Zaveri / Erik Lindahl / Ryan E Hibbs /
Abstract: Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The α3β4 nicotinic receptor subtype forms the principal relay between the central and ...Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The α3β4 nicotinic receptor subtype forms the principal relay between the central and peripheral nervous systems in the autonomic ganglia. This receptor is also expressed focally in brain areas that affect reward circuits and addiction. Here, we present structures of the α3β4 nicotinic receptor in lipidic and detergent environments, using functional reconstitution to define lipids appropriate for structural analysis. The structures of the receptor in complex with nicotine, as well as the α3β4-selective ligand AT-1001, complemented by molecular dynamics, suggest principles of agonist selectivity. The structures further reveal much of the architecture of the intracellular domain, where mutagenesis experiments and simulations define residues governing ion conductance.
History
DepositionJul 19, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseSep 11, 2019-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20489.png

Downloads & links

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Map

FileDownload / File: emd_20489.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 300 pix.
= 267. Å		0.89 Å/pix.
x 300 pix.
= 267. Å		0.89 Å/pix.
x 300 pix.
= 267. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0125 / Movie #1: 0.0125
Minimum - Maximum-0.035960086 - 0.05024397
Average (Standard dev.)0.00027391332 (±0.0018914673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 267.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.890.890.89
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z267.000267.000267.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0360.0500.000

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Supplemental data

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Half map: #2

Fileemd_20489_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_20489_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Human alpha3beta4 nicotinic receptor in complex with Fab fragment...

EntireName: Human alpha3beta4 nicotinic receptor in complex with Fab fragments and bound to nicotine
Components
  • Complex: Human alpha3beta4 nicotinic receptor in complex with Fab fragments and bound to nicotine

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Supramolecule #1: Human alpha3beta4 nicotinic receptor in complex with Fab fragment...

SupramoleculeName: Human alpha3beta4 nicotinic receptor in complex with Fab fragments and bound to nicotine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Fab fragments generated by proteolytic cleavage of IgG antibody
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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

Concentration6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
1.0 mMC9H15O6PTris(2-carboxyethyl)phosphine
1.0 mMC10H14N2Nicotine
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1020 / Average exposure time: 2.0 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 57013 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 231484
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: De novo initial model from Relion
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 74820
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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