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- EMDB-65744: human VMAT2 in complex with MDMA -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65744
Titlehuman VMAT2 in complex with MDMA
Map data
Sample
  • Complex: human VMAT2 in complex with MDMA
    • Protein or peptide: Synaptic vesicular amine transporter
  • Ligand: (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine
Keywordstransporter C with 3 / 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 / clathrin-sculpted monoamine transport vesicle membrane / monoamine:proton antiporter activity / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Norepinephrine 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 / clathrin-sculpted monoamine transport vesicle membrane / monoamine:proton antiporter activity / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Norepinephrine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / serotonin uptake / monoamine transmembrane transporter activity / histamine secretion by mast cell / dopaminergic synapse / neurotransmitter transport / negative regulation of reactive oxygen species biosynthetic process / secretory granule membrane / terminal bouton / synaptic vesicle membrane / synaptic vesicle / chemical synaptic transmission / axon / dendrite / 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: 2.89 Å
AuthorsWu D / Jiang DH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: To Be Published
Title: transporter C with 3
Authors: Wu D / Jiang DH
History
DepositionAug 7, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65744.png

Downloads & links

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Map

FileDownload / File: emd_65744.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.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.395
Minimum - Maximum-2.0745811 - 2.6867712
Average (Standard dev.)-0.000619126 (±0.044947535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65744_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65744_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 : human VMAT2 in complex with MDMA

EntireName: human VMAT2 in complex with MDMA
Components
  • Complex: human VMAT2 in complex with MDMA
    • Protein or peptide: Synaptic vesicular amine transporter
  • Ligand: (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine

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Supramolecule #1: human VMAT2 in complex with MDMA

SupramoleculeName: human VMAT2 in complex with MDMA / 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: 55.749352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALSELALVR WLQESRRSRK LILFIVFLAL LLDNMLLTVV VPIIPSYLYS IKHEKNATEI QTARPVHTAS ISDSFQSIFS YYDNSTMVT GNATRDLTLH QTATQHMVTN ASAVPSDCPS EDKDLLNENV QVGLLFASKA TVQLITNPFI GLLTNRIGYP I PIFAGFCI ...String:
MALSELALVR WLQESRRSRK LILFIVFLAL LLDNMLLTVV VPIIPSYLYS IKHEKNATEI QTARPVHTAS ISDSFQSIFS YYDNSTMVT GNATRDLTLH QTATQHMVTN ASAVPSDCPS EDKDLLNENV QVGLLFASKA TVQLITNPFI GLLTNRIGYP I PIFAGFCI MFVSTIMFAF SSSYAFLLIA RSLQGIGSSC SSVAGMGMLA SVYTDDEERG NVMGIALGGL AMGVLVGPPF GS VLYEFVG KTAPFLVLAA LVLLDGAIQL FVLQPSRVQP ESQKGTPLTT LLKDPYILIA AGSICFANMG IAMLEPALPI WMM ETMCSR KWQLGVAFLP ASISYLIGTN IFGILAHKMG RWLCALLGMI IVGVSILCIP FAKNIYGLIA PNFGVGFAIG MVDS SMMPI MGYLVDLRHV SVYGSVYAIA DVAFCMGYAI GPSAGGAIAK AIGFPWLMTI IGIIDILFAP LCFFLRSPPA KEEKM AILM DHNCPIKTKM YTQNNIQSYP IGEDEESESD

UniProtKB: Synaptic vesicular amine transporter

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Macromolecule #2: (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine

MacromoleculeName: (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine / type: ligand / ID: 2 / Number of copies: 1 / Formula: B41
Molecular weightTheoretical: 193.242 Da
Chemical component information

ChemComp-B41:
(2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 281302
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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