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- PDB-8zms: Acetylcholine-bound VAChT -

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Basic information

Entry
Database: PDB / ID: 8zms
TitleAcetylcholine-bound VAChT
ComponentsMaltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7
KeywordsTRANSPORT PROTEIN / VAChT / SLC18A3 / Acetylcholine
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
ACETYLCHOLINE / Maltose/maltodextrin-binding periplasmic protein / Vesicular acetylcholine transporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang, Z. / Zhang, Y. / Dai, F. / Zhang, Y.X. / Lee, C.-H.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8512
Polymers112,7051
Non-polymers1461
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / VAChT / Solute carrier family ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / VAChT / Solute carrier family 18 member 3


Mass: 112705.180 Da / Num. of mol.: 1 / Mutation: A520E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: malE, b4034, JW3994, SLC18A3, VACHT / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: Q16572
#2: Chemical ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: VAChT / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.06 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (strain K12) (bacteria)83333
21Homo sapiens (human)9606
31synthetic construct (others)32630
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.25
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201313 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0062989
ELECTRON MICROSCOPYf_angle_d1.0984082
ELECTRON MICROSCOPYf_dihedral_angle_d6.1181761
ELECTRON MICROSCOPYf_chiral_restr0.055497
ELECTRON MICROSCOPYf_plane_restr0.01501

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