8XTY | pdb_00008xty

Structure of human VAChT in complex with vesamicol

• PDB DOI: https://doi.org/10.2210/pdb8XTY/pdb
• EM Map EMD-38653: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN/INHIBITOR
• Organism(s): Homo sapiens, Aequorea victoria
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-01-12 Released: 2024-12-25 
• Deposition Author(s): Zhao, Y., Ma, Q., Dong, Y., Meng, Y.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Binding mechanism and antagonism of the vesicular acetylcholine transporter VAChT.

Ma, Q., Ma, K., Dong, Y., Meng, Y., Zhao, J., Li, R., Bai, Q., Wu, D., Jiang, D., Sun, J., Zhao, Y.

(2025) Nat Struct Mol Biol 32: 818-827

• PubMed: 39806024 
• DOI: https://doi.org/10.1038/s41594-024-01462-9
• Primary Citation Related Structures: 
  8XTW, 8XTX, 8XTY


• PubMed 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. 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.

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Organizational Affiliation: 
• Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders and National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 92.2 kDa 
• Atom Count: 2,895 
• Modeled Residue Count: 382 
• Deposited Residue Count: 851 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vesicular acetylcholine transporter,Green fluorescent protein,antibody	A	851	Homo sapiens, Aequorea victoria	Mutation(s): 0  Gene Names: SLC18A3, VACHT, GFP
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for Q16572 (Homo sapiens) Explore Q16572  Go to UniProtKB:  Q16572
PHAROS:  Q16572 GTEx:  ENSG00000187714
UniProt Groups	P42212Q16572

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LWL (Subject of Investigation/LOI)	B [auth A]	vesamicol C17 H25 N O YSSBJODGIYRAMI-IRXDYDNUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Zhao, Y., Ma, Q., Dong, Y., Meng, Y.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release
  
• Version 1.1: 2025-06-11
  Changes: Data collection, Database references
• Version 2.0: 2025-07-16
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary