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- PDB-9kqm: Cryo-EM structure of human VAChT in complex with VSM -

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Basic information

Entry
Database: PDB / ID: 9kqm
TitleCryo-EM structure of human VAChT in complex with VSM
ComponentsSoluble cytochrome b562,Vesicular acetylcholine transporter
KeywordsTRANSPORT PROTEIN / transporter / VAChT
Function / homology
Function and homology information


acetylcholine:proton antiporter activity / acetylcholine uptake / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / AP-1 adaptor complex / positive regulation of neuromuscular junction development / Acetylcholine Neurotransmitter Release Cycle / monoamine:proton antiporter activity / AP-2 adaptor complex / serotonin uptake ...acetylcholine:proton antiporter activity / acetylcholine uptake / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / AP-1 adaptor complex / positive regulation of neuromuscular junction development / Acetylcholine Neurotransmitter Release Cycle / monoamine:proton antiporter activity / AP-2 adaptor complex / serotonin uptake / positive regulation of acetylcholine secretion, neurotransmission / neurotransmitter transport / positive regulation of long-term synaptic potentiation / clathrin-coated endocytic vesicle membrane / electron transport chain / terminal bouton / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle membrane / Clathrin-mediated endocytosis / chemical synaptic transmission / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Cytochrome b562 / Cytochrome b562 / MFS transporter superfamily / Cytochrome c/b562
Similarity search - Domain/homology
: / Soluble cytochrome b562 / Vesicular acetylcholine transporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, W. / Wei, F. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human VAChT in complex with VSM
Authors: Zhang, W. / Wei, F. / Zhang, Y.
History
DepositionNov 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data 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: Soluble cytochrome b562,Vesicular acetylcholine transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5852
Polymers69,3261
Non-polymers2591
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Soluble cytochrome b562,Vesicular acetylcholine transporter / Cytochrome b-562 / VAChT / Solute carrier family 18 member 3


Mass: 69325.781 Da / Num. of mol.: 1 / Mutation: M8W,H103I,R107L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, SLC18A3, VACHT / Production host: Homo sapiens (human) / References: UniProt: P0ABE7, UniProt: Q16572
#2: Chemical ChemComp-A1ER3 / (1R,2R)-2-(4-phenylpiperidin-1-yl)cyclohexan-1-ol


Mass: 259.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25NO / Feature type: SUBJECT OF INVESTIGATION
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: VAChT / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172916 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063125
ELECTRON MICROSCOPYf_angle_d0.7524277
ELECTRON MICROSCOPYf_dihedral_angle_d12.85439
ELECTRON MICROSCOPYf_chiral_restr0.046522
ELECTRON MICROSCOPYf_plane_restr0.006529

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