9WJH | pdb_00009wjh

Spiroindoline-bound human VAChT


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of VAChT inhibition by spiroindolines and alkylsulfones.

Zhang, Y.Zhang, Z.

(2025) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.10.005
  • Primary Citation of Related Structures:  
    9WJH, 9WJI

  • PubMed Abstract: 

    Cholinergic signaling relies on the vesicular acetylcholine transporter (VAChT) to package acetylcholine (ACh) into synaptic vesicles. VAChT dysfunction is implicated in neurological and neuromuscular disorders, including Alzheimer's disease and myasthenia gravis, yet current inhibitors such as vesamicol suffer from off-target effects. Here, we present cryo-EM structures of human VAChT bound to two inhibitors, spiroindoline and alkylsulfone, revealing their divergent binding modes that converge in occupying the central substrate pocket. Mutagenesis studies identify conserved residues critical for inhibitor binding. These findings elucidate the molecular mechanisms by which VAChT binds structurally distinct inhibitors, providing a blueprint for designing optimized therapeutics. Furthermore, species-specific structural variations identified here suggest opportunities to develop selective insecticides through ortholog-targeted inhibition. Taken together, this work bridges mechanistic insights with therapeutic and agricultural applications, advancing precision tools for modulating the cholinergic system.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPins1,047Escherichia coli K-12Homo sapienssynthetic construct
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994SLC18A3VACHT
UniProt & NIH Common Fund Data Resources
Find proteins for Q16572 (Homo sapiens)
Explore Q16572 
Go to UniProtKB:  Q16572
PHAROS:  Q16572
GTEx:  ENSG00000187714 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16572
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EWS (Subject of Investigation/LOI)
Query on A1EWS

Download Ideal Coordinates CCD File 
B [auth A](6-bromanylpyridin-3-yl)-[1'-[(~{E})-3-(4-chlorophenyl)prop-2-enyl]-5-fluoranyl-spiro[2~{H}-indole-3,4'-piperidine]-1-yl]methanone
C27 H24 Br Cl F N3 O
RDXPBCTWNYFBFI-OWOJBTEDSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32471252

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references