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- PDB-9nx0: Alpha7-nicotinic acetylcholine receptor bound to conotoxin ImI -

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Basic information

Entry
Database: PDB / ID: 9nx0
TitleAlpha7-nicotinic acetylcholine receptor bound to conotoxin ImI
Components
  • Alpha-conotoxin ImI
  • Neuronal acetylcholine receptor subunit alpha-7
KeywordsMEMBRANE PROTEIN / ion channel / toxin
Function / homology
Function and homology information


sensory processing / synaptic transmission involved in micturition / host cell postsynaptic membrane / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / regulation of amyloid fibril formation ...sensory processing / synaptic transmission involved in micturition / host cell postsynaptic membrane / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory / ion channel regulator activity / cation channel complex / dendritic spine organization / chloride channel regulator activity / acetylcholine binding / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / neurotransmitter receptor complex / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / positive regulation of protein metabolic process / response to amyloid-beta / ligand-gated ion channel signaling pathway / monoatomic ion channel activity / modulation of excitatory postsynaptic potential / negative regulation of tumor necrosis factor production / plasma membrane raft / toxic substance binding / monoatomic ion transport / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / positive regulation of excitatory postsynaptic potential / positive regulation of long-term synaptic potentiation / response to nicotine / regulation of membrane potential / excitatory postsynaptic potential / synapse organization / cognition / calcium channel activity / memory / intracellular calcium ion homeostasis / positive regulation of angiogenesis / transmembrane signaling receptor activity / calcium ion transport / amyloid-beta binding / toxin activity / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / response to hypoxia / learning or memory / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / neuron projection / postsynapse / positive regulation of cell population proliferation / dendrite / synapse / endoplasmic reticulum membrane / signal transduction / protein homodimerization activity / extracellular region / membrane / plasma membrane
Similarity search - Function
Conotoxin, alpha-type, conserved site / 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 ...Conotoxin, alpha-type, conserved site / 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
Chem-POV / Neuronal acetylcholine receptor subunit alpha-7 / Alpha-conotoxin ImI
Similarity search - Component
Biological speciesHomo sapiens (human)
Conus imperialis (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsStowell, M.H.B. / Hibbs, R.E. / Noviello, C.M. / Bhattacharjee, B.
Funding support United States, 3items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Alpha-conotoxin ImI
H: Alpha-conotoxin ImI
I: Alpha-conotoxin ImI
J: Alpha-conotoxin ImI
F: Alpha-conotoxin ImI
A: Neuronal acetylcholine receptor subunit alpha-7
B: Neuronal acetylcholine receptor subunit alpha-7
E: Neuronal acetylcholine receptor subunit alpha-7
D: Neuronal acetylcholine receptor subunit alpha-7
C: Neuronal acetylcholine receptor subunit alpha-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,53530
Polymers277,38510
Non-polymers9,15020
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Alpha-conotoxin ImI / Alpha-CTx ImI


Mass: 1356.601 Da / Num. of mol.: 5 / Fragment: residues 5-16 / Source method: obtained synthetically / Source: (synth.) Conus imperialis (invertebrata) / References: UniProt: P50983
#2: Protein
Neuronal acetylcholine receptor subunit alpha-7


Mass: 54120.375 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA7, NACHRA7 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P36544
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of conotoxin ImI and human Alpha7 nicotinic Acetylcholine receptorCOMPLEX#1-#20MULTIPLE SOURCES
2Alpha7 nicotinic Acetylcholine receptorCOMPLEX#21RECOMBINANT
3Conotoxin ImICOMPLEX#11SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Conus imperialis (invertebrata)35631
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 30000 nm / Nominal defocus min: 5000 nm / Calibrated defocus min: 5000 nm
Image recordingElectron dose: 55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80193 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 7KOO

7koo


Accession code: 7KOO / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317290
ELECTRON MICROSCOPYf_angle_d0.56123545
ELECTRON MICROSCOPYf_dihedral_angle_d6.3222419
ELECTRON MICROSCOPYf_chiral_restr0.0412680
ELECTRON MICROSCOPYf_plane_restr0.0052895

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