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Basic information

Entry
Database: PDB / ID: 8xtx
Titlestructure of a protein
ComponentsGreen fluorescent protein,Vesicular acetylcholine transporter,antibody
KeywordsTRANSPORT PROTEIN / Transporter / Membrane protein
Function / homology
Function and homology information


acetylcholine:proton antiporter activity / acetylcholine uptake / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / positive regulation of neuromuscular junction development / AP-1 adaptor complex / monoamine:proton antiporter activity / Acetylcholine Neurotransmitter Release Cycle / AP-2 adaptor complex / positive regulation of acetylcholine secretion, neurotransmission ...acetylcholine:proton antiporter activity / acetylcholine uptake / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / positive regulation of neuromuscular junction development / AP-1 adaptor complex / monoamine:proton antiporter activity / Acetylcholine Neurotransmitter Release Cycle / AP-2 adaptor complex / positive regulation of acetylcholine secretion, neurotransmission / serotonin uptake / neurotransmitter transport / bioluminescence / positive regulation of long-term synaptic potentiation / generation of precursor metabolites and energy / clathrin-coated endocytic vesicle membrane / terminal bouton / synaptic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / chemical synaptic transmission / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Vesicular acetylcholine transporter
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhao, Y. / Ma, Q. / Dong, Y. / Meng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Binding mechanism and antagonism of the vesicular acetylcholine transporter VAChT.
Authors: Qiao Ma / Kunpeng Ma / Yanli Dong / Yufei Meng / Jun Zhao / Renjie Li / Qinru Bai / Di Wu / Daohua Jiang / Jianyuan Sun / Yan Zhao /
Abstract: The vesicular acetylcholine transporter (VAChT) has a pivotal role in packaging and transporting acetylcholine for exocytotic release, serving as a vital component of cholinergic neurotransmission. ...The vesicular acetylcholine transporter (VAChT) has a pivotal role in packaging and transporting acetylcholine for exocytotic release, serving as a vital component of cholinergic neurotransmission. Dysregulation of its function can result in neurological disorders. It also serves as a target for developing radiotracers to quantify cholinergic neuron deficits in neurodegenerative conditions. Here we unveil the cryo-electron microscopy structures of human VAChT in its apo state, the substrate acetylcholine-bound state and the inhibitor vesamicol-bound state. These structures assume a lumen-facing conformation, offering a clear depiction of architecture of VAChT. The acetylcholine-bound structure provides a detailed understanding of how VAChT recognizes its substrate, shedding light on the coupling mechanism of protonation and substrate binding. Meanwhile, the vesamicol-bound structure reveals the binding mode of vesamicol to VAChT, laying the structural foundation for the design of the next generation of radioligands targeting VAChT.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein,Vesicular acetylcholine transporter,antibody


Theoretical massNumber of molelcules
Total (without water)89,5631
Polymers89,5631
Non-polymers00
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: Antibody Green fluorescent protein,Vesicular acetylcholine transporter,antibody / VAChT / Solute carrier family 18 member 3


Mass: 89562.812 Da / Num. of mol.: 1
Mutation: S30R,Y39N,F64L,S65T,QQ80R,F99S,N105T,Y145F,M153T,V163A,I171V,A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, SLC18A3, VACHT / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: P42212, UniProt: Q16572
Has protein modificationN

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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: transporter / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115468 / Symmetry type: POINT

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