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- EMDB-16169: Alpha7-nAChR extracellular ligand-binding domain (alpha7-ECD)in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-16169
TitleAlpha7-nAChR extracellular ligand-binding domain (alpha7-ECD)in complex with alpha-bungarotoxin.
Map data
Sample
  • Complex: Alpha7-nAChR (Nicotinic acetylcholine receptor of alpha7 type) extracellular ligand-binding domain
    • Complex: alpha-bungarotoxin
Biological speciesHomo sapiens (human) / Naja kaouthia (monocled cobra)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsChesnokov YM / Kamyshinsky RA
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20163 Russian Federation
CitationJournal: Commun Biol / Year: 2022
Title: Membrane-mediated interaction of non-conventional snake three-finger toxins with nicotinic acetylcholine receptors.
Authors: Zakhar O Shenkarev / Yuri M Chesnokov / Maxim M Zaigraev / Anton O Chugunov / Dmitrii S Kulbatskii / Milita V Kocharovskaya / Alexander S Paramonov / Maxim L Bychkov / Mikhail A Shulepko / ...Authors: Zakhar O Shenkarev / Yuri M Chesnokov / Maxim M Zaigraev / Anton O Chugunov / Dmitrii S Kulbatskii / Milita V Kocharovskaya / Alexander S Paramonov / Maxim L Bychkov / Mikhail A Shulepko / Dmitry E Nolde / Roman A Kamyshinsky / Evgeniy O Yablokov / Alexey S Ivanov / Mikhail P Kirpichnikov / Ekaterina N Lyukmanova /
Abstract: Nicotinic acetylcholine receptor of α7 type (α7-nAChR) presented in the nervous and immune systems and epithelium is a promising therapeutic target for cognitive disfunctions and cancer treatment. ...Nicotinic acetylcholine receptor of α7 type (α7-nAChR) presented in the nervous and immune systems and epithelium is a promising therapeutic target for cognitive disfunctions and cancer treatment. Weak toxin from Naja kaouthia venom (WTX) is a non-conventional three-finger neurotoxin, targeting α7-nAChR with weak affinity. There are no data on interaction mode of non-conventional neurotoxins with nAChRs. Using α-bungarotoxin (classical three-finger neurotoxin with high affinity to α7-nAChR), we showed applicability of cryo-EM to study complexes of α7-nAChR extracellular ligand-binding domain (α7-ECD) with toxins. Using cryo-EM structure of the α7-ECD/WTX complex, together with NMR data on membrane active site in the WTX molecule and mutagenesis data, we reconstruct the structure of α7-nAChR/WTX complex in the membrane environment. WTX interacts at the entrance to the orthosteric site located at the receptor intersubunit interface and simultaneously forms the contacts with the membrane surface. WTX interaction mode with α7-nAChR significantly differs from α-bungarotoxin's one, which does not contact the membrane. Our study reveals the important role of the membrane for interaction of non-conventional neurotoxins with the nicotinic receptors.
History
DepositionNov 18, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16169.png

Downloads & links

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Map

FileDownload / File: emd_16169.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 192 pix.
= 165.12 Å		0.86 Å/pix.
x 192 pix.
= 165.12 Å		0.86 Å/pix.
x 192 pix.
= 165.12 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.3873855 - 0.5401769
Average (Standard dev.)0.00019207218 (±0.018418483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 165.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16169_msk_1.map
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Half map: #2

Fileemd_16169_half_map_1.map
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Half map: #1

Fileemd_16169_half_map_2.map
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Sample components

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Entire : Alpha7-nAChR (Nicotinic acetylcholine receptor of alpha7 type) ex...

EntireName: Alpha7-nAChR (Nicotinic acetylcholine receptor of alpha7 type) extracellular ligand-binding domain
Components
  • Complex: Alpha7-nAChR (Nicotinic acetylcholine receptor of alpha7 type) extracellular ligand-binding domain
    • Complex: alpha-bungarotoxin

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Supramolecule #1: Alpha7-nAChR (Nicotinic acetylcholine receptor of alpha7 type) ex...

SupramoleculeName: Alpha7-nAChR (Nicotinic acetylcholine receptor of alpha7 type) extracellular ligand-binding domain
type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10 KDa

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Supramolecule #2: alpha-bungarotoxin

SupramoleculeName: alpha-bungarotoxin / type: complex / ID: 2 / Chimera: Yes / Parent: 1
Source (natural)Organism: Naja kaouthia (monocled cobra)

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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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
20.0 mMNH2C(CH2OH)3HClTris hydrochloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Cs corrector
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2245 / Average exposure time: 2.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
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

Particle selectionNumber selected: 1517534
Startup modelType of model: INSILICO MODEL / In silico model: ab ititio in CryoSparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 27813
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 56589 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsPDB 4HQP was used to rigid body fit
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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