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 9YWV | pdb_00009ywv

Serotonin-bound structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9YWV

This is version 1.0 of the entry. See complete history. 

Literature

Cooperative mechanism of neurotransmitter recognition and transport by the human vesicular polyamine transporter.

Guo, Y., Yang, G., Chai, J., Shanklin, J., Liu, B., Lu, M.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-75564-x
  • Primary Citation Related Structures: 
    9YWU, 9YWV

  • PubMed Abstract: 

    Human vesicular polyamine transporter (hVPAT) from the SLC18 antiporter family sequesters polyamine neuromodulators into secretory vesicles in exchange for H + in the brain, thereby sustaining learning and memory formation. As a potential therapeutic target for combatting psychostimulant use disorder, hVPAT (or SLC18B1) regulates the homeostasis of monoamine neurotransmitters via an unknown mechanism. Here we report the cryo-electron microscopy structures of hVPAT in complexes with histamine and serotonin, revealing up to three distinct neurotransmitter-binding sites within the lumen-facing SLC18 antiporter. Complementary proteo-liposome-based transport and ligand-binding assays suggest that hVPAT transports multiple monoamine neurotransmitters simultaneously, exhibiting variable H⁺/substrate stoichiometry and positive cooperativity. Unexpectedly, this cooperativity appears to arise from the direct interactions between the bound histamine or serotonin molecules, which also contributes to substrate selectivity. In this work, our findings uncover a hitherto unidentified modality for monoamine neurotransmitter recognition and offer unprecedented insights into the general principles governing membrane transport.


  • Organizational Affiliation: 
    • Center for Proteomics & Molecular Therapeutics, Rosalind Franklin University of Medicine & Science, North Chicago, IL, USA.

Macromolecule Content 

  • Total Structure Weight: 49.25 kDa 
  • Atom Count: 2,984 
  • Modeled Residue Count: 391 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MFS-type transporter SLC18B1456Homo sapiensMutation(s): 0 
Gene Names: SLC18B1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NT16 (Homo sapiens)
Explore Q6NT16 
Go to UniProtKB:  Q6NT16
PHAROS:  Q6NT16
GTEx:  ENSG00000146409 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NT16
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-10-07 
  • Deposition Author(s): Lu, M., Liu, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM145642

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-07
    Type: Initial release