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- PDB-9wjh: Spiroindoline-bound human VAChT -

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Basic information

Entry
Database: PDB / ID: 9wjh
TitleSpiroindoline-bound human VAChT
ComponentsMaltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPins
KeywordsTRANSPORT PROTEIN / VAChT / SLC18A3 / Acetylcholine / Spiroindoline
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 / Acetylcholine Neurotransmitter Release Cycle / monoamine:proton antiporter activity / positive regulation of acetylcholine secretion, neurotransmission / AP-2 adaptor complex ...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 / Acetylcholine Neurotransmitter Release Cycle / monoamine:proton antiporter activity / 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 / positive regulation of long-term synaptic potentiation / cell chemotaxis / 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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / MFS transporter superfamily / 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 K-12 (bacteria)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang, Z. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471252 China
CitationJournal: To Be Published
Title: Structural basis of VAChT inhibition by spiroindolines and alkylsulfones
Authors: Zhang, Z. / Zhang, Y.
History
DepositionAug 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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,DARPins
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2462
Polymers112,7051
Non-polymers5411
Water543
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,DARPins / 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Strain: K-12 / Gene: malE, b4034, JW3994, SLC18A3, VACHT / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: Q16572
#2: Chemical ChemComp-A1EWS / (6-bromanylpyridin-3-yl)-[1'-[(~{E})-3-(4-chlorophenyl)prop-2-enyl]-5-fluoranyl-spiro[2~{H}-indole-3,4'-piperidine]-1-yl]methanone


Mass: 540.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24BrClFN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: human VAChT in complex with spiroindoline / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.25
SpecimenConc.: 8 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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
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: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 328769 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0073087
ELECTRON MICROSCOPYf_angle_d1.114219
ELECTRON MICROSCOPYf_dihedral_angle_d11.0471088
ELECTRON MICROSCOPYf_chiral_restr0.056503
ELECTRON MICROSCOPYf_plane_restr0.009520

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