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- EMDB-38653: structure of a protein -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38653
Titlestructure of a protein
Map data
Sample
  • Complex: transporter
    • Protein or peptide: Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,antibody
  • Ligand: vesamicol
KeywordsTransporter / Membrane protein / TRANSPORT PROTEIN / TRANSPORT PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


acetylcholine:proton antiporter activity / acetylcholine uptake / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / positive regulation of neuromuscular junction development / AP-1 adaptor complex / monoamine:proton antiporter activity / Acetylcholine Neurotransmitter Release Cycle / AP-2 adaptor complex / positive regulation of acetylcholine secretion, neurotransmission ...acetylcholine:proton antiporter activity / acetylcholine uptake / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / positive regulation of neuromuscular junction development / AP-1 adaptor complex / monoamine:proton antiporter activity / Acetylcholine Neurotransmitter Release Cycle / AP-2 adaptor complex / positive regulation of acetylcholine secretion, neurotransmission / serotonin uptake / neurotransmitter transport / bioluminescence / positive regulation of long-term synaptic potentiation / generation of precursor metabolites and energy / clathrin-coated endocytic vesicle membrane / terminal bouton / synaptic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / chemical synaptic transmission / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Vesicular acetylcholine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhao Y / Ma Q / Dong Y / Meng Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Binding mechanism and antagonism of the vesicular acetylcholine transporter VAChT.
Authors: Qiao Ma / Kunpeng Ma / Yanli Dong / Yufei Meng / Jun Zhao / Renjie Li / Qinru Bai / Di Wu / Daohua Jiang / Jianyuan Sun / Yan Zhao /
Abstract: The vesicular acetylcholine transporter (VAChT) has a pivotal role in packaging and transporting acetylcholine for exocytotic release, serving as a vital component of cholinergic neurotransmission. ...The vesicular acetylcholine transporter (VAChT) has a pivotal role in packaging and transporting acetylcholine for exocytotic release, serving as a vital component of cholinergic neurotransmission. Dysregulation of its function can result in neurological disorders. It also serves as a target for developing radiotracers to quantify cholinergic neuron deficits in neurodegenerative conditions. Here we unveil the cryo-electron microscopy structures of human VAChT in its apo state, the substrate acetylcholine-bound state and the inhibitor vesamicol-bound state. These structures assume a lumen-facing conformation, offering a clear depiction of architecture of VAChT. The acetylcholine-bound structure provides a detailed understanding of how VAChT recognizes its substrate, shedding light on the coupling mechanism of protonation and substrate binding. Meanwhile, the vesamicol-bound structure reveals the binding mode of vesamicol to VAChT, laying the structural foundation for the design of the next generation of radioligands targeting VAChT.
History
DepositionJan 12, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38653.png

Downloads & links

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Map

FileDownload / File: emd_38653.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 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: 0.53
Minimum - Maximum-2.3668022 - 4.1759634
Average (Standard dev.)-0.0013944671 (±0.0945654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-127-127
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38653_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_38653_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 : transporter

EntireName: transporter
Components
  • Complex: transporter
    • Protein or peptide: Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,antibody
  • Ligand: vesamicol

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Supramolecule #1: transporter

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

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Macromolecule #1: Green fluorescent protein,Vesicular acetylcholine transporter,Gre...

MacromoleculeName: Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,Green ...Name: Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,Green fluorescent protein,Vesicular acetylcholine transporter,antibody
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.562812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATNG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFKIR ...String:
MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATNG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFKIR HNVEDGSVQL ADHYQQNTPI GDGPVLLPDN HYLSTQSVLS KDPNEKRDHM VLLEFVTAAG IEPRRQRRLV LV IVCVALL LDNMLYMVIV PIVPDYIAHM RGGGEGPTRT PEVWEPTLPL PTPANASAYT ANTSASPTAA WPAGSALRPR YPT ESEDVK IGVLFASKAI LQLLVNPLSG PFIDRMSYDV PLLIGLGVMF ASTVLFAFAE DYATLFAARS LQGLGSAFAD TSGI AMIAD KYPEEPERSR ALGVALAFIS FGSLVAPPFG GILYEFAGKR VPFLVLAAVS LFDALLLLAV AKPFSAAARA RANLP VGTP IHRLMLDPYI AVVAGALTTC NIPLAFLEPT IATWMKHTMA ASEWEMGMAW LPAFVPHVLG VYLTVRLAAR YPHLQW LYG ALGLAVIGAS SCIVPACRSF APLVVSLCGL CFGIALVDTA LLPTLAFLVD VRHVSVYGSV YAIADISYSV AYALGPI VA GHIVHSLGFE QLSLGMGLAN LLYAPVLLLL RNVGLLTGSG QVQLVESGGA LVQPGGSLRL SCAASGFPVN RYSMRWYR Q APGKEREWVA GMSSAGDRSS YEDSVKGRFT ISRDDARNTV YLQMNSLKPE DTAVYYCNVN VGFEYWGQGT QVTVSMGWS HPQFEKGGGS GGGSGGSAWS HPQFEK

UniProtKB: Green fluorescent protein, Vesicular acetylcholine transporter

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Macromolecule #2: vesamicol

MacromoleculeName: vesamicol / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1LWL
Molecular weightTheoretical: 259.386 Da

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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

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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 396134
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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