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- PDB-9gu0: Human adult muscle nAChR in resting state in detergent with alpha... -

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Entry
Database: PDB / ID: 9gu0
TitleHuman adult muscle nAChR in resting state in detergent with alpha-bungarotoxin
Components
  • (Acetylcholine receptor subunit ...) x 4
  • Alpha-bungarotoxin
  • Fab35 heavy chain
  • Fab35 light chain
KeywordsMEMBRANE PROTEIN / Ligand-gated ion channel / nicotinic receptor / pLGIC / cys-loop receptor
Function / homology
Function and homology information


postsynaptic membrane organization / skeletal muscle tissue growth / musculoskeletal movement / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / behavioral response to nicotine / acetylcholine receptor inhibitor activity ...postsynaptic membrane organization / skeletal muscle tissue growth / musculoskeletal movement / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / behavioral response to nicotine / acetylcholine receptor inhibitor activity / neuromuscular synaptic transmission / acetylcholine-gated monoatomic cation-selective channel activity / muscle cell development / ion channel regulator activity / acetylcholine binding / synaptic transmission, cholinergic / monoatomic cation transmembrane transporter activity / nervous system process / acetylcholine receptor signaling pathway / ligand-gated monoatomic ion channel activity / postsynaptic specialization membrane / neuromuscular process / muscle cell cellular homeostasis / neuromuscular junction development / monoatomic cation transport / membrane depolarization / skeletal muscle contraction / neuronal action potential / muscle contraction / bioluminescence / generation of precursor metabolites and energy / response to nicotine / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / neuromuscular junction / neuron cellular homeostasis / transmembrane signaling receptor activity / channel activity / toxin activity / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / neuron projection / synapse / cell surface / signal transduction / extracellular region / plasma membrane
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Nicotinic acetylcholine receptor / Snake toxin-like superfamily / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain ...Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Nicotinic acetylcholine receptor / Snake toxin-like superfamily / 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 / Green fluorescent protein, GFP / 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 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Acetylcholine receptor subunit beta / Green fluorescent protein / Alpha-bungarotoxin / Acetylcholine receptor subunit epsilon / Acetylcholine receptor subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
Aequorea victoria (jellyfish)
Bungarus multicinctus (many-banded krait)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLi, A. / Pike, A.C.W. / Chi, G. / Webster, R. / Maxwell, S. / Liu, W. / Beeson, D. / Sauer, D.B. / Dong, Y.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust102161/Z/13/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/Y012623/1 United Kingdom
CitationJournal: Cell Rep / Year: 2025
Title: Structures of the human adult muscle-type nicotinic receptor in resting and desensitized states.
Authors: Anna Li / Ashley C W Pike / Richard Webster / Susan Maxwell / Wei-Wei Liu / Gamma Chi / Jacqueline Palace / David Beeson / David B Sauer / Yin Yao Dong /
Abstract: Muscle-type nicotinic acetylcholine receptor (AChR) is the key signaling molecule in neuromuscular junctions. Here, we present the structures of full-length human adult receptors in complex with ...Muscle-type nicotinic acetylcholine receptor (AChR) is the key signaling molecule in neuromuscular junctions. Here, we present the structures of full-length human adult receptors in complex with Fab35 in α-bungarotoxin (αBuTx)-bound resting states and ACh-bound desensitized states. In addition to identifying the conformational changes during recovery from desensitization, we also used electrophysiology to probe the effects of eight previously unstudied AChR genetic variants found in patients with congenital myasthenic syndrome (CMS), revealing they cause either slow- or fast-channel CMS characterized by prolonged or abbreviated ion channel bursts. The combined kinetic and structural data offer a better understanding of both the AChR state transition and the pathogenic mechanisms of disease variants.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholine receptor subunit alpha
B: Acetylcholine receptor subunit beta
C: Fab35 light chain
D: Acetylcholine receptor subunit delta
E: Acetylcholine receptor subunit epsilon,Green fluorescent protein
F: Fab35 heavy chain
G: Fab35 light chain
H: Fab35 heavy chain
J: Alpha-bungarotoxin
L: Acetylcholine receptor subunit alpha
I: Alpha-bungarotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,89418
Polymers402,16711
Non-polymers5,7277
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Acetylcholine receptor subunit ... , 4 types, 5 molecules ALBDE

#1: Protein Acetylcholine receptor subunit alpha


Mass: 49747.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA1, ACHRA, CHNRA / Plasmid: TLCV2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P02708
#2: Protein Acetylcholine receptor subunit beta


Mass: 54596.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNB1, ACHRB, CHRNB / Plasmid: TLCV2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P11230
#4: Protein Acetylcholine receptor subunit delta


Mass: 56915.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRND, ACHRD / Plasmid: TLCV2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q07001
#5: Protein Acetylcholine receptor subunit epsilon,Green fluorescent protein


Mass: 80603.750 Da / Num. of mol.: 1
Mutation: EGFP insertion between residues R344 and A345 in the M3-M4 intracellular loop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Gene: CHRNE, ACHRE, GFP / Plasmid: TLCV2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q04844, UniProt: P42212

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Protein , 1 types, 2 molecules JI

#7: Protein Alpha-bungarotoxin / Alpha-Bgtx / Alpha-Btx / Alpha-bungarotoxin / isoform A31 / Alpha-BTX A31 / Alpha-BgTx(A31) / Alpha- ...Alpha-Bgtx / Alpha-Btx / Alpha-bungarotoxin / isoform A31 / Alpha-BTX A31 / Alpha-BgTx(A31) / Alpha-bungarotoxin (A31) / BGTX A31 / Alpha-elapitoxin-Bm2a / Alpha-EPTX-Bm2a / Long neurotoxin 1


Mass: 8005.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60615

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Antibody , 2 types, 4 molecules CGFH

#3: Antibody Fab35 light chain


Mass: 23392.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): Hybridoma / Production host: Rattus norvegicus (Norway rat)
#6: Antibody Fab35 heavy chain


Mass: 23879.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): Hybridoma / Production host: Rattus norvegicus (Norway rat)

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Sugars , 6 types, 7 molecules

#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1276.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#11: 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.: 1
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
#12: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#13: 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.: 1 / Source method: obtained synthetically / 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

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Details

Has ligand of interestN
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

ComponentName: Human adult muscle nAChR in resting state in detergent with alpha-bungarotoxin
Type: COMPLEX / Details: nAChR in complex with alpha-bungarotoxin and Fab35 / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: 0.402 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F / Plasmid: TLCV2
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 0.013% DDM, 0.0013% CHS
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
30.013 %n-Dodecyl-beta-D-MaltopyaranosideC24H46O111
40.0013 %Cholesteryl hemisuccinateC31H50O41
SpecimenConc.: 1.68 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.35 K / Details: blot time 2s, blot force -10

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: objective aperture 70 um
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.71 sec. / Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 18672
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2EPUimage acquisition
4cryoSPARC3.3.1CTF correction
7UCSF ChimeraX1.6.1model fitting
8Coot0.9.8model fitting
9ISOLDEmodel fitting
11cryoSPARC3.3.1initial Euler assignment
12cryoSPARC3.3.1final Euler assignment
13RELION3.1.3classification
14cryoSPARC3.3.13D reconstruction
15PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1249235 / Details: Extracted by topaz picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31022 / Algorithm: FOURIER SPACE / Details: Non-uniform refinement / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial fitting of alphafold models using chimeraX followed by manual rebuilding in COOT and final refinement in ISOLDE and PHENIX
Atomic model building
ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11P027081AlphaFoldin silico model
21P112302AlphaFoldin silico model
31Q070013AlphaFoldin silico model
41Q048444AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 116.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002423433
ELECTRON MICROSCOPYf_angle_d0.497232053
ELECTRON MICROSCOPYf_chiral_restr0.04223859
ELECTRON MICROSCOPYf_plane_restr0.00454000
ELECTRON MICROSCOPYf_dihedral_angle_d12.66658390

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