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- EMDB-36637: Human VMAT2 complex with ketanserin -

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Basic information

Entry
Database: EMDB / ID: EMD-36637
TitleHuman VMAT2 complex with ketanserin
Map data
Sample
  • Complex: transporter1
    • Protein or peptide: Synaptic vesicular amine transporter
  • Ligand: 3-[2-[4-(4-fluorophenyl)carbonylpiperidin-1-yl]ethyl]-1~{H}-quinazoline-2,4-dione
Keywordstransporter1 / TRANSPORT PROTEIN
Function / homology
Function and homology information


serotonin secretion by mast cell / somato-dendritic dopamine secretion / histamine uptake / aminergic neurotransmitter loading into synaptic vesicle / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Dopamine Neurotransmitter Release Cycle ...serotonin secretion by mast cell / somato-dendritic dopamine secretion / histamine uptake / aminergic neurotransmitter loading into synaptic vesicle / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / serotonin uptake / dopamine transport / monoamine transmembrane transporter activity / histamine secretion by mast cell / monoamine transport / dopaminergic synapse / SLC-mediated transport of neurotransmitters / neurotransmitter transport / negative regulation of reactive oxygen species biosynthetic process / secretory granule membrane / response to amphetamine / post-embryonic development / locomotory behavior / response to toxic substance / terminal bouton / synaptic vesicle / synaptic vesicle membrane / chemical synaptic transmission / axon / intracellular membrane-bounded organelle / dendrite / centrosome / membrane / plasma 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
Synaptic vesicular amine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsJiang DH / Wu D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271272 China
CitationJournal: Nature / Year: 2024
Title: Transport and inhibition mechanisms of human VMAT2.
Authors: Di Wu / Qihao Chen / Zhuoya Yu / Bo Huang / Jun Zhao / Yuhang Wang / Jiawei Su / Feng Zhou / Rui Yan / Na Li / Yan Zhao / Daohua Jiang /
Abstract: Vesicular monoamine transporter 2 (VMAT2) accumulates monoamines in presynaptic vesicles for storage and exocytotic release, and has a vital role in monoaminergic neurotransmission. Dysfunction of ...Vesicular monoamine transporter 2 (VMAT2) accumulates monoamines in presynaptic vesicles for storage and exocytotic release, and has a vital role in monoaminergic neurotransmission. Dysfunction of monoaminergic systems causes many neurological and psychiatric disorders, including Parkinson's disease, hyperkinetic movement disorders and depression. Suppressing VMAT2 with reserpine and tetrabenazine alleviates symptoms of hypertension and Huntington's disease, respectively. Here we describe cryo-electron microscopy structures of human VMAT2 complexed with serotonin and three clinical drugs at 3.5-2.8 Å, demonstrating the structural basis for transport and inhibition. Reserpine and ketanserin occupy the substrate-binding pocket and lock VMAT2 in cytoplasm-facing and lumen-facing states, respectively, whereas tetrabenazine binds in a VMAT2-specific pocket and traps VMAT2 in an occluded state. The structures in three distinct states also reveal the structural basis of the VMAT2 transport cycle. Our study establishes a structural foundation for the mechanistic understanding of substrate recognition, transport, drug inhibition and pharmacology of VMAT2 while shedding light on the rational design of potential therapeutic agents.
History
DepositionJun 21, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36637.png

Downloads & links

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Map

FileDownload / File: emd_36637.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.383
Minimum - Maximum-0.9026173 - 1.8855422
Average (Standard dev.)0.0009269341 (±0.084333345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36637_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_36637_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : transporter1

EntireName: transporter1
Components
  • Complex: transporter1
    • Protein or peptide: Synaptic vesicular amine transporter
  • Ligand: 3-[2-[4-(4-fluorophenyl)carbonylpiperidin-1-yl]ethyl]-1~{H}-quinazoline-2,4-dione

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Supramolecule #1: transporter1

SupramoleculeName: transporter1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Synaptic vesicular amine transporter

MacromoleculeName: Synaptic vesicular amine transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.086848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SRKLILFIVF LALLLDNMLL TVVVPIIPSY LYSIKHEKNA TEIQTARPVH TASISDSFQS IFSYYDNSTM VTGNATRDLT LHQTATQHM VTNASAVPSD CPSEDKDLLN ENVQVGLLFA SKATVQLITN PFIGLLTNRI GYPIPIFAGF CIMFVSTIMF A FSSSYAFL ...String:
SRKLILFIVF LALLLDNMLL TVVVPIIPSY LYSIKHEKNA TEIQTARPVH TASISDSFQS IFSYYDNSTM VTGNATRDLT LHQTATQHM VTNASAVPSD CPSEDKDLLN ENVQVGLLFA SKATVQLITN PFIGLLTNRI GYPIPIFAGF CIMFVSTIMF A FSSSYAFL LIARSLQGIG SSCSSVAGMG MLASVYTDDE ERGNVMGIAL GGLAMGVLVG PPFGSVLYEF VGKTAPFLVL AA LVLLDGA IQLFVLQPSR VQPESQKGTP LTTLLKDPYI LIAAGSICFA NMGIAMLEPA LPIWMMETMC SRKWQLGVAF LPA SISYLI GTNIFGILAH KMGRWLCALL GMIIVGVSIL CIPFAKNIYG LIAPNFGVGF AIGMVDSSMM PIMGYLVDLR HVSV YGSVY AIADVAFCMG YAIGPSAGGA IAKAIGFPWL MTIIGIIDIL FAPLCFFLRS PP

UniProtKB: Synaptic vesicular amine transporter

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Macromolecule #2: 3-[2-[4-(4-fluorophenyl)carbonylpiperidin-1-yl]ethyl]-1~{H}-quina...

MacromoleculeName: 3-[2-[4-(4-fluorophenyl)carbonylpiperidin-1-yl]ethyl]-1~{H}-quinazoline-2,4-dione
type: ligand / ID: 2 / Number of copies: 1 / Formula: UYX
Molecular weightTheoretical: 395.427 Da
Chemical component information

ChemComp-UYX:
3-[2-[4-(4-fluorophenyl)carbonylpiperidin-1-yl]ethyl]-1~{H}-quinazoline-2,4-dione

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 504617
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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