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- EMDB-60255: Acetylcholine-bound VAChT -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-60255
TitleAcetylcholine-bound VAChT
Map data
Sample
  • Complex: VAChT
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7
  • Ligand: ACETYLCHOLINE
KeywordsVAChT / SLC18A3 / Acetylcholine / TRANSPORT PROTEIN
Function / homology
Function and homology information


acetylcholine:proton antiporter activity / acetylcholine uptake / positive regulation of neuromuscular junction development / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / monoamine:proton antiporter activity / AP-1 adaptor complex / Acetylcholine Neurotransmitter Release Cycle / positive regulation of acetylcholine secretion, neurotransmission / AP-2 adaptor complex ...acetylcholine:proton antiporter activity / acetylcholine uptake / positive regulation of neuromuscular junction development / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / monoamine:proton antiporter activity / AP-1 adaptor complex / Acetylcholine Neurotransmitter Release Cycle / positive regulation of acetylcholine secretion, neurotransmission / AP-2 adaptor complex / serotonin uptake / neurotransmitter transport / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of long-term synaptic potentiation / clathrin-coated endocytic vesicle membrane / terminal bouton / synaptic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / outer membrane-bounded periplasmic space / chemical synaptic transmission / periplasmic space / DNA damage response / membrane / plasma membrane
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Vesicular acetylcholine transporter
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang Z / Zhang Y / Dai F / Zhang YX / Lee C-H
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Res / Year: 2024
Title: Structural insights into VAChT neurotransmitter recognition and inhibition.
Authors: Yang Zhang / Fei Dai / Nanhao Chen / Dong Zhou / Chia-Hsueh Lee / Chen Song / Yixiao Zhang / Zhe Zhang /
History
DepositionMay 23, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60255.png

Downloads & links

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Map

FileDownload / File: emd_60255.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.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.6915747 - 0.9476891
Average (Standard dev.)0.0008065769 (±0.019692918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60255_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_60255_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 : VAChT

EntireName: VAChT
Components
  • Complex: VAChT
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7
  • Ligand: ACETYLCHOLINE

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Supramolecule #1: VAChT

SupramoleculeName: VAChT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetyl...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 112.70518 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEITP DKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN LQEPYFTWPL I AADGGYAF ...String:
MEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEITP DKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN LQEPYFTWPL I AADGGYAF KYENGKYDIK DVGVDNAGAK AGLTFLIDLI KNKHMNADTD YSIAEAAFNK GETAMTINGP WAWSNIDTSK VN YGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EELVKDPRVA ATM ENAQKG EIMPNIPQMS AFWYAVRTAV INAASGRQTV DAALAAAQAE EEKRKAEEEK RKLVLVIVCV ALLLDNMLYM VIVP IVPDY IAHMRGGGEG PTRTPEVWEP TLPLPTPANA SAYTANTSAS PTAAWPAGSA LRPRYPTESE DVKIGVLFAS KAILQ LLVN PLSGPFIDRM SYDVPLLIGL GVMFASTVLF AFAEDYATLF AARSLQGLGS AFADTSGIAM IADKYPEEPE RSRALG VAL AFISFGSLVA PPFGGILYEF AGKRVPFLVL AAVSLFDALL LLAVAKPFSA AARARANLPV GTPIHRLMLD PYIAVVA GA LTTCNIPLAF LEPTIATWMK HTMAASEWEM GMAWLPAFVP HVLGVYLTVR LAARYPHLQW LYGALGLAVI GASSCIVP A CRSFAPLVVS LCGLCFGIAL VDTALLPTLA FLVDVRHVSV YGSVYAIADI SYSVAYALGP IVAGHIVHSL GFEQLSLGM GLANLLYAPV LLLLRNVGLL TRSRSERDVL LDEPPQGLYD AVRLRERPVS GQDGEPRSPP GPFDECEDDG GGGSGGGGSD LGRKLLEAA RAGQLDEVRI LLANGADVNA ADNTGTTPLH LAAYSGHLEI VEVLLKHGAD VDASDVFGYT PLHLAAYWGH L EIVEVLLK NGADVNAMDS DGMTPLHLAA KWGYLEIVEV LLKHGADVNA QDKFGKTAFD ISIDNGNEDL AEILQKLNLE GG SLEVLFQ

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Vesicular acetylcholine transporter

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Macromolecule #2: ACETYLCHOLINE

MacromoleculeName: ACETYLCHOLINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACH
Molecular weightTheoretical: 146.207 Da
Chemical component information

ChemComp-ACH:
ACETYLCHOLINE / neurotransmitter*YM

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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

Concentration10 mg/mL
BufferpH: 7.25
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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201313
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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