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- EMDB-14065: Torpedo muscle-type nicotinic acetylcholine receptor - carbamylch... -

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Basic information

Entry
Database: EMDB / ID: EMD-14065
TitleTorpedo muscle-type nicotinic acetylcholine receptor - carbamylcholine-bound conformation
Map dataSharpened map out of refinement
Sample
  • Complex: Torpedo muscle-type nicotinic acetylcholine receptor
    • Protein or peptide: Acetylcholine receptor subunit alpha
    • Protein or peptide: Acetylcholine receptor subunit beta
    • Protein or peptide: Acetylcholine receptor subunit delta
    • Protein or peptide: Acetylcholine receptor subunit gamma
  • Ligand: 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordspentameric ligand-gated ion channel / nicotinic receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


acetylcholine-gated monoatomic cation-selective channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynaptic membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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
Acetylcholine receptor subunit alpha / Acetylcholine receptor subunit beta / Acetylcholine receptor subunit gamma / Acetylcholine receptor subunit delta
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsZarkadas E / Pebay-Peyroula E
Funding support Canada, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)637733 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)113312 Canada
CitationJournal: Neuron / Year: 2022
Title: Conformational transitions and ligand-binding to a muscle-type nicotinic acetylcholine receptor.
Authors: Eleftherios Zarkadas / Eva Pebay-Peyroula / Mackenzie John Thompson / Guy Schoehn / Tomasz Uchański / Jan Steyaert / Christophe Chipot / Francois Dehez / John Edward Baenziger / Hugues Nury /
Abstract: Fast synaptic communication requires receptors that respond to the presence of neurotransmitter by opening an ion channel across the post-synaptic membrane. The muscle-type nicotinic acetylcholine ...Fast synaptic communication requires receptors that respond to the presence of neurotransmitter by opening an ion channel across the post-synaptic membrane. The muscle-type nicotinic acetylcholine receptor from the electric fish, Torpedo, is the prototypic ligand-gated ion channel, yet the structural changes underlying channel activation remain undefined. Here we use cryo-EM to solve apo and agonist-bound structures of the Torpedo nicotinic receptor embedded in a lipid nanodisc. Using both a direct biochemical assay to define the conformational landscape and molecular dynamics simulations to assay flux through the pore, we correlate structures with functional states and elucidate the motions that lead to pore activation of a heteromeric nicotinic receptor. We highlight an underappreciated role for the complementary subunit in channel gating, establish the structural basis for the differential agonist affinities of α/δ versus α /γ sites, and explain why nicotine is less potent at muscle nicotinic receptors compared to neuronal ones.
History
DepositionDec 19, 2021-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.217
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.217
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ql6
  • Surface level: 0.217
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_14065.png

Downloads & links

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Map

FileDownload / File: emd_14065.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map out of refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 293.12 Å		1.15 Å/pix.
x 256 pix.
= 293.12 Å		1.15 Å/pix.
x 256 pix.
= 293.12 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.217 / Movie #1: 0.217
Minimum - Maximum-0.5953592 - 1.2690027
Average (Standard dev.)0.0016444514 (±0.043421835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 293.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1451.1451.145
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z293.120293.120293.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5951.2690.002

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Supplemental data

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Mask #1

Fileemd_14065_msk_1.map
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AxesZYX

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Mask #2

Fileemd_14065_msk_2.map
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Histogram (log scale)

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Additional map: Unsharpened map from refinement

Fileemd_14065_additional_1.map
AnnotationUnsharpened map from refinement
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_14065_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_14065_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Torpedo muscle-type nicotinic acetylcholine receptor

EntireName: Torpedo muscle-type nicotinic acetylcholine receptor
Components
  • Complex: Torpedo muscle-type nicotinic acetylcholine receptor
    • Protein or peptide: Acetylcholine receptor subunit alpha
    • Protein or peptide: Acetylcholine receptor subunit beta
    • Protein or peptide: Acetylcholine receptor subunit delta
    • Protein or peptide: Acetylcholine receptor subunit gamma
  • Ligand: 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Torpedo muscle-type nicotinic acetylcholine receptor

SupramoleculeName: Torpedo muscle-type nicotinic acetylcholine receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Native receptor reconstituted in lipidic nanodiscs.
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Acetylcholine receptor subunit alpha

MacromoleculeName: Acetylcholine receptor subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 50.168164 KDa
SequenceString: SEHETRLVAN LLENYNKVIR PVEHHTHFVD ITVGLQLIQL ISVDEVNQIV ETNVRLRQQW IDVRLRWNPA DYGGIKKIRL PSDDVWLPD LVLYNNADGD FAIVHMTKLL LDYTGKIMWT PPAIFKSYCE IIVTHFPFDQ QNCTMKLGIW TYDGTKVSIS P ESDRPDLS ...String:
SEHETRLVAN LLENYNKVIR PVEHHTHFVD ITVGLQLIQL ISVDEVNQIV ETNVRLRQQW IDVRLRWNPA DYGGIKKIRL PSDDVWLPD LVLYNNADGD FAIVHMTKLL LDYTGKIMWT PPAIFKSYCE IIVTHFPFDQ QNCTMKLGIW TYDGTKVSIS P ESDRPDLS TFMESGEWVM KDYRGWKHWV YYTCCPDTPY LDITYHFIMQ RIPLYFVVNV IIPCLLFSFL TGLVFYLPTD SG EKMTLSI SVLLSLTVFL LVIVELIPST SSAVPLIGKY MLFTMIFVIS SIIITVVVIN THHRSPSTHT MPQWVRKIFI DTI PNVMFF STMKRASKEK QENKIFADDI DISDISGKQV TGEVIFQTPL IKNPDVKSAI EGVKYIAEHM KSDEESSNAA EEWK YVAMV IDHILLCVFM LICIIGTVSV FAGRLIELSQ EG

UniProtKB: Acetylcholine receptor subunit alpha

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Macromolecule #2: Acetylcholine receptor subunit beta

MacromoleculeName: Acetylcholine receptor subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 53.731773 KDa
SequenceString: SVMEDTLLSV LFETYNPKVR PAQTVGDKVT VRVGLTLTNL LILNEKIEEM TTNVFLNLAW TDYRLQWDPA AYEGIKDLRI PSSDVWQPD IVLMNNNDGS FEITLHVNVL VQHTGAVSWQ PSAIYRSSCT IKVMYFPFDW QNCTMVFKSY TYDTSEVTLQ H ALDAKGER ...String:
SVMEDTLLSV LFETYNPKVR PAQTVGDKVT VRVGLTLTNL LILNEKIEEM TTNVFLNLAW TDYRLQWDPA AYEGIKDLRI PSSDVWQPD IVLMNNNDGS FEITLHVNVL VQHTGAVSWQ PSAIYRSSCT IKVMYFPFDW QNCTMVFKSY TYDTSEVTLQ H ALDAKGER EVKEIVINKD AFTENGQWSI EHKPSRKNWR SDDPSYEDVT FYLIIQRKPL FYIVYTIIPC ILISILAILV FY LPPDAGE KMSLSISALL AVTVFLLLLA DKVPETSLSV PIIIRYLMFI MILVAFSVIL SVVVLNLHHR SPNTHTMPNW IRQ IFIETL PPFLWIQRPV TTPSPDSKPT IISRANDEYF IRKPAGDFVC PVDNARVAVQ PERLFSEMKW HLNGLTQPVT LPQD LKEAV EAIKYIAEQL ESASEFDDLK KDWQYVAMVA DRLFLYVFFV ICSIGTFSIF LDASHNVPPD NPFA

UniProtKB: Acetylcholine receptor subunit beta

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Macromolecule #3: Acetylcholine receptor subunit delta

MacromoleculeName: Acetylcholine receptor subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 57.625711 KDa
SequenceString: VNEEERLIND LLIVNKYNKH VRPVKHNNEV VNIALSLTLS NLISLKETDE TLTSNVWMDH AWYDHRLTWN ASEYSDISIL RLPPELVWI PDIVLQNNND GQYHVAYFCN VLVRPNGYVT WLPPAIFRSS CPINVLYFPF DWQNCSLKFT ALNYDANEIT M DLMTDTID ...String:
VNEEERLIND LLIVNKYNKH VRPVKHNNEV VNIALSLTLS NLISLKETDE TLTSNVWMDH AWYDHRLTWN ASEYSDISIL RLPPELVWI PDIVLQNNND GQYHVAYFCN VLVRPNGYVT WLPPAIFRSS CPINVLYFPF DWQNCSLKFT ALNYDANEIT M DLMTDTID GKDYPIEWII IDPEAFTENG EWEIIHKPAK KNIYPDKFPN GTNYQDVTFY LIIRRKPLFY VINFITPCVL IS FLASLAF YLPAESGEKM STAISVLLAQ AVFLLLTSQR LPETALAVPL IGKYLMFIMS LVTGVIVNCG IVLNFHFRTP STH VLSTRV KQIFLEKLPR ILHMSRADES EQPDWQNDLK LRRSSSVGYI SKAQEYFNIK SRSELMFEKQ SERHGLVPRV TPRI GFGNN NENIAASDQL HDEIKSGIDS TNYIVKQIKE KNAYDEEVGN WNLVGQTIDR LSMFIITPVM VLGTIFIFVM GNFNH PPAK PFEGDPFDYS SDHPRCA

UniProtKB: Acetylcholine receptor subunit delta

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Macromolecule #4: Acetylcholine receptor subunit gamma

MacromoleculeName: Acetylcholine receptor subunit gamma / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 56.335684 KDa
SequenceString: ENEEGRLIEK LLGDYDKRII PAKTLDHIID VTLKLTLTNL ISLNEKEEAL TTNVWIEIQW NDYRLSWNTS EYEGIDLVRI PSELLWLPD VVLENNVDGQ FEVAYYANVL VYNDGSMYWL PPAIYRSTCP IAVTYFPFDW QNCSLVFRSQ TYNAHEVNLQ L SAEEGEAV ...String:
ENEEGRLIEK LLGDYDKRII PAKTLDHIID VTLKLTLTNL ISLNEKEEAL TTNVWIEIQW NDYRLSWNTS EYEGIDLVRI PSELLWLPD VVLENNVDGQ FEVAYYANVL VYNDGSMYWL PPAIYRSTCP IAVTYFPFDW QNCSLVFRSQ TYNAHEVNLQ L SAEEGEAV EWIHIDPEDF TENGEWTIRH RPAKKNYNWQ LTKDDTDFQE IIFFLIIQRK PLFYIINIIA PCVLISSLVV LV YFLPAQA GGQKCTLSIS VLLAQTIFLF LIAQKVPETS LNVPLIGKYL IFVMFVSMLI VMNCVIVLNV SLRTPNTHSL SEK IKHLFL GFLPKYLGMQ LEPSEETPEK PQPRRRSSFG IMIKAEEYIL KKPRSELMFE EQKDRHGLKR VNKMTSDIDI GTTV DLYKD LANFAPEIKS CVEACNFIAK STKEQNDSGS ENENWVLIGK VIDKACFWIA LLLFSIGTLA IFLTGHFNQV PEFPF PGDP RKYVP

UniProtKB: Acetylcholine receptor subunit gamma

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Macromolecule #8: 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM

MacromoleculeName: 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM / type: ligand / ID: 8 / Number of copies: 2 / Formula: CCE
Molecular weightTheoretical: 147.195 Da
Chemical component information

ChemComp-CCE:
2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.65 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47646
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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