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- PDB-8xty: Structure of human VAChT in complex with vesamicol -

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Basic information

Entry
Database: PDB / ID: 8xty
TitleStructure of human VAChT in complex with vesamicol
ComponentsVesicular acetylcholine transporter,Green fluorescent protein,antibody
KeywordsTRANSPORT PROTEIN/INHIBITOR / Transporter / Membrane protein / TRANSPORT PROTEIN / TRANSPORT PROTEIN-INHIBITOR complex
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 / Acetylcholine Neurotransmitter Release Cycle / monoamine:proton antiporter activity / positive regulation of acetylcholine secretion, neurotransmission / AP-2 adaptor complex ...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 / Acetylcholine Neurotransmitter Release Cycle / monoamine:proton antiporter activity / positive regulation of acetylcholine secretion, neurotransmission / AP-2 adaptor complex / 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 speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,2042
Polymers91,9441
Non-polymers2591
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 Vesicular acetylcholine transporter,Green fluorescent protein,antibody / VAChT / Solute carrier family 18 member 3


Mass: 91944.422 Da / Num. of mol.: 1
Mutation: S30R,Y39N,F64L,S65T,Q80R,F99S,N105T,Y145F,M153T,V163A,I171V,A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Gene: SLC18A3, VACHT, GFP / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: Q16572, UniProt: P42212
#2: Chemical ChemComp-A1LWL / vesamicol / (1~{S},2~{S})-2-(4-phenylpiperidin-1-yl)cyclohexan-1-ol / 2-(4-Phenylpiperidino)cyclohexanol


Mass: 259.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25NO / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: #1 / 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 396134 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032968
ELECTRON MICROSCOPYf_angle_d0.554058
ELECTRON MICROSCOPYf_dihedral_angle_d7.39415
ELECTRON MICROSCOPYf_chiral_restr0.039497
ELECTRON MICROSCOPYf_plane_restr0.006496

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