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- PDB-9ywu: Histamine-bound structure -

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Basic information

Entry
Database: PDB / ID: 9ywu
TitleHistamine-bound structure
ComponentsMFS-type transporter SLC18B1
KeywordsMEMBRANE PROTEIN / membrane transporter / neurotransmitter transporter
Function / homology
Function and homology information


polyamine:proton antiporter activity / spermidine transport / spermine transport / monoamine:proton antiporter activity / serotonin uptake / transmembrane transporter activity / secretory granule membrane / synaptic vesicle membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
HISTAMINE / MFS-type transporter SLC18B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLu, M. / Liu, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145642 United States
CitationJournal: Nat Commun / Year: 2026
Title: Cooperative mechanism of neurotransmitter recognition and transport by the human vesicular polyamine transporter.
Authors: Yi Guo / Ge Yang / Jin Chai / John Shanklin / Bin Liu / Min Lu /
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 ...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.
History
DepositionOct 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MFS-type transporter SLC18B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2304
Polymers48,8961
Non-polymers3333
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein MFS-type transporter SLC18B1 / Solute carrier family 18 member B1 / Vesicular polyamine transporter / VPAT


Mass: 48896.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC18B1, C6orf192 / Production host: Insecta environmental sample (insect) / References: UniProt: Q6NT16
#2: Chemical ChemComp-HSM / HISTAMINE


Mass: 111.145 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9N3 / Comment: neurotransmitter, hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: membrane transport protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.050 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Insecta environmental sample (insect)
Buffer solutionpH: 8
SpecimenConc.: 3 mg/ml / Embedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7Cootmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127728 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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