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- EMDB-49899: Muscle-type nicotinic acetylcholine receptor bound to conotoxin ImII -

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Basic information

Entry
Database: EMDB / ID: EMD-49899
TitleMuscle-type nicotinic acetylcholine receptor bound to conotoxin ImII
Map data
Sample
  • Complex: Complex of conotoxin ImII and human muscle-type nicotinic acetyclcholine receptor
    • Complex: Human muscle-type nicotinic acetyclcholine receptor
      • Protein or peptide: Acetylcholine receptor subunit alpha
      • Protein or peptide: Acetylcholine receptor subunit delta
      • Protein or peptide: Acetylcholine receptor subunit beta
      • Protein or peptide: Acetylcholine receptor subunit gamma
    • Complex: Conotoxin ImII
      • Protein or peptide: Alpha-conotoxin ImII
  • Ligand: 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsion channel / toxin / MEMBRANE PROTEIN
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / ion channel regulator activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / toxin activity / postsynaptic membrane / extracellular region
Similarity search - Function
Alpha-conotoxin family signature. / 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 ...Alpha-conotoxin family signature. / 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 / Alpha-conotoxin ImII
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray) / Conus imperialis (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsStowell MHB / Hibbs RE / Noviello CM / Bhattacharjee B
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS120496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136430 United States
CitationJournal: Structure / Year: 2025
Title: Shape-shifting conotoxins reveal divergent pore-targeting mechanisms in nicotinic receptors.
Authors: Biddut Bhattacharjee / Colleen M Noviello / Md Mahfuzur Rahman / John P Mayer / Joanna Gajewiak / J Michael McIntosh / Ryan E Hibbs / Michael H B Stowell /
Abstract: The neuronal α7 nicotinic acetylcholine receptor (α7-nAChR) and muscle-type nicotinic acetylcholine receptor (mt-nAChR) are pivotal in synaptic signaling within the brain and the neuromuscular ...The neuronal α7 nicotinic acetylcholine receptor (α7-nAChR) and muscle-type nicotinic acetylcholine receptor (mt-nAChR) are pivotal in synaptic signaling within the brain and the neuromuscular junction respectively. Additionally, they are both targets of a wide range of drugs and toxins. Here, we utilize cryo-EM to delineate structures of these nAChRs in complex with the conotoxins ImI and ImII from Conus imperialis. Despite nominal sequence differences, ImI and ImII exhibit discrete binding preferences and adopt drastically different conformational states upon binding. ImI engages the orthosteric sites of α7-nAChR, while ImII forms distinct pore-bound complexes with both α7-nAChR and mt-nAChR. Strikingly, ImII adopts a compact globular conformation that binds as a monomer to the α7-nAChR pore and as an oblate dimer to the mt-nAChR pore. These structures advance our understanding of nAChR-ligand interactions and the subtle sequence variations that result in dramatically altered functional outcomes in small peptide toxins.
History
DepositionMar 25, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49899.png

Downloads & links

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Map

FileDownload / File: emd_49899.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.)
0.87 Å/pix.
x 300 pix.
= 261.6 Å		0.87 Å/pix.
x 300 pix.
= 261.6 Å		0.87 Å/pix.
x 300 pix.
= 261.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.872 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.04761855 - 0.12691306
Average (Standard dev.)0.00056125637 (±0.004773368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_49899_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49899_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of conotoxin ImII and human muscle-type nicotinic acetycl...

EntireName: Complex of conotoxin ImII and human muscle-type nicotinic acetyclcholine receptor
Components
  • Complex: Complex of conotoxin ImII and human muscle-type nicotinic acetyclcholine receptor
    • Complex: Human muscle-type nicotinic acetyclcholine receptor
      • Protein or peptide: Acetylcholine receptor subunit alpha
      • Protein or peptide: Acetylcholine receptor subunit delta
      • Protein or peptide: Acetylcholine receptor subunit beta
      • Protein or peptide: Acetylcholine receptor subunit gamma
    • Complex: Conotoxin ImII
      • Protein or peptide: Alpha-conotoxin ImII
  • Ligand: 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Complex of conotoxin ImII and human muscle-type nicotinic acetycl...

SupramoleculeName: Complex of conotoxin ImII and human muscle-type nicotinic acetyclcholine receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: Human muscle-type nicotinic acetyclcholine receptor

SupramoleculeName: Human muscle-type nicotinic acetyclcholine receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Tetronarce californica (Pacific electric ray)

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Supramolecule #3: Conotoxin ImII

SupramoleculeName: Conotoxin ImII / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Conus imperialis (invertebrata) / Synthetically produced: Yes

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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: 49.869895 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 FAGRKIELS

UniProtKB: Acetylcholine receptor subunit alpha

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Macromolecule #2: Acetylcholine receptor subunit delta

MacromoleculeName: Acetylcholine receptor subunit delta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 57.4555 KDa
SequenceString: NEEERLINDL LIVNKYNKHV RPVKHNNEVV NIALSLTLSN LISLKETDET LTSNVWMDHA WYDHRLTWNA SEYSDISILR LPPELVWIP DIVLQNNNDG QYHVAYFCNV LVRPNGYVTW LPPAIFRSSC PINVLYFPFD WQNCSLKFTA LNYDANEITM D LMTDTIDG ...String:
NEEERLINDL LIVNKYNKHV RPVKHNNEVV NIALSLTLSN LISLKETDET LTSNVWMDHA WYDHRLTWNA SEYSDISILR LPPELVWIP DIVLQNNNDG QYHVAYFCNV LVRPNGYVTW LPPAIFRSSC PINVLYFPFD WQNCSLKFTA LNYDANEITM D LMTDTIDG KDYPIEWIII DPEAFTENGE WEIIHKPAKK NIYPDKFPNG TNYQDVTFYL IIRRKPLFYV INFITPCVLI SF LASLAFY LPAESGEKMS TAISVLLAQA VFLLLTSQRL PETALAVPLI GKYLMFIMSL VTGVIVNCGI VLNFHFRTPS THV LSTRVK QIFLEKLPRI LHMSRADESE QPDWQNDLKL RRSSSVGYIS KAQEYFNIKS RSELMFEKQS ERHGLVPRVT PRIG FGNNN ENIAASDQLH DEIKSGIDST NYIVKQIKEK NAYDEEVGNW NLVGQTIDRL SMFIITPVMV LGTIFIFVMG NFNHP PAKP FEGDPFDYSS DHPRC

UniProtKB: Acetylcholine receptor subunit delta

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Macromolecule #3: Acetylcholine receptor subunit beta

MacromoleculeName: Acetylcholine receptor subunit beta / type: protein_or_peptide / ID: 3 / 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 #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 #5: Alpha-conotoxin ImII

MacromoleculeName: Alpha-conotoxin ImII / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Conus imperialis (invertebrata)
Molecular weightTheoretical: 1.516822 KDa
SequenceString:
ACCSDRRCRW RC(NH2)

UniProtKB: Alpha-conotoxin ImII

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Macromolecule #11: 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM

MacromoleculeName: 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM / type: ligand / ID: 11 / 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 #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 5.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 30.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 128448
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7koo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9nx2:
Muscle-type nicotinic acetylcholine receptor bound to conotoxin ImII

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