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- EMDB-73562: Serotonin-bound structure -

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Basic information

Entry
Database: EMDB / ID: EMD-73562
TitleSerotonin-bound structure
Map data
Sample
  • Complex: membrane transporter
    • Protein or peptide: MFS-type transporter SLC18B1
  • Ligand: SEROTONIN
  • Ligand: water
Keywordsmembrane transporter / neurotransmitter transporter / MEMBRANE PROTEIN
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
MFS-type transporter SLC18B1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLu M / Liu B
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73562.png

Downloads & links

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Map

FileDownload / File: emd_73562.map.gz / Format: CCP4 / Size: 36.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 212 pix.
= 212.48 Å		1 Å/pix.
x 212 pix.
= 212.48 Å		1 Å/pix.
x 212 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.00226 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-0.34172076 - 20.781523
Average (Standard dev.)0.082576446 (±0.7687168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions212212212
Spacing212212212
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73562_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73562_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : membrane transporter

EntireName: membrane transporter
Components
  • Complex: membrane transporter
    • Protein or peptide: MFS-type transporter SLC18B1
  • Ligand: SEROTONIN
  • Ligand: water

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Supramolecule #1: membrane transporter

SupramoleculeName: membrane transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

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Macromolecule #1: MFS-type transporter SLC18B1

MacromoleculeName: MFS-type transporter SLC18B1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.896363 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: MEALGDLEGP RAPGGDDPAG SAGETPGWLS REQVFVLISA ASVNLGSMMC YSILGPFFPK EAEKKGASNT IIGMIFGCFA LFELLASLV FGNYLVHIGA KFMFVAGMFV SGGVTILFGV LDRVPDGPVF IAMCFLVRVM DAVSFAAAMT ASSSILAKAF P NNVATVLG ...String:
MEALGDLEGP RAPGGDDPAG SAGETPGWLS REQVFVLISA ASVNLGSMMC YSILGPFFPK EAEKKGASNT IIGMIFGCFA LFELLASLV FGNYLVHIGA KFMFVAGMFV SGGVTILFGV LDRVPDGPVF IAMCFLVRVM DAVSFAAAMT ASSSILAKAF P NNVATVLG SLETFSGLGL ILGPPVGGFL YQSFGYEVPF IVLGCVVLLM VPLNMYILPN YESDPGEHSF WKLIALPKVG LI AFVINSL SSCFGFLDPT LSLFVLEKFN LPAGYVGLVF LGMALSYAIS SPLFGLLSDK RPPLRKWLLV FGNLITAGCY MLL GPVPIL HIKSQLWLLV LILVVSGLSA GMSIIPTFPE ILSCAHENGF EEGLSTLGLV SGLFSAMWSI GAFMGPTLGG FLYE KIGFE WAAAIQGLWA LISGLAMGLF YLLEYSRRKR SKSQNILSTE EERTTLLPNE T

UniProtKB: MFS-type transporter SLC18B1

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Macromolecule #2: SEROTONIN

MacromoleculeName: SEROTONIN / type: ligand / ID: 2 / Number of copies: 2 / Formula: SRO
Molecular weightTheoretical: 176.215 Da
Chemical component information

ChemComp-SRO:
SEROTONIN / neurotransmitter*YM

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 82664
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9ywv:
Serotonin-bound structure

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