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- PDB-9wix: Cryo-EM structure of VGLUT3 in apo state -

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Basic information

Entry
Database: PDB / ID: 9wix
TitleCryo-EM structure of VGLUT3 in apo state
ComponentsVesicular glutamate transporter 3
KeywordsTRANSPORT PROTEIN / vesicle / glutamate transporter / apo state
Function / homology
Function and homology information


regulation of acetylcholine uptake / SLC-mediated transport of neurotransmitters / L-glutamate uniporter activity / pericellular basket / sodium:phosphate symporter activity / sodium-dependent phosphate transport / positive regulation of glutamate uptake involved in transmission of nerve impulse / clathrin-sculpted glutamate transport vesicle membrane / basal dendrite / L-glutamate import ...regulation of acetylcholine uptake / SLC-mediated transport of neurotransmitters / L-glutamate uniporter activity / pericellular basket / sodium:phosphate symporter activity / sodium-dependent phosphate transport / positive regulation of glutamate uptake involved in transmission of nerve impulse / clathrin-sculpted glutamate transport vesicle membrane / basal dendrite / L-glutamate import / glial limiting end-foot / neurotransmitter loading into synaptic vesicle / L-glutamate transmembrane transporter activity / L-glutamate transmembrane transport / phosphate ion homeostasis / neurotransmitter transmembrane transporter activity / neural retina development / apical dendrite / regulation of synapse structure or activity / chloride channel activity / cochlea development / chloride channel complex / multivesicular body / sensory perception of sound / excitatory synapse / axon terminus / synaptic transmission, glutamatergic / synaptic vesicle membrane / synaptic vesicle / perikaryon / neuronal cell body / dendrite / glutamatergic synapse / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
CHOLESTEROL HEMISUCCINATE / Vesicular glutamate transporter 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsQu, Q.H. / Chao, Y.L. / Yang, C.H. / Wang, X. / Zhou, Z.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171194 China
CitationJournal: To Be Published
Title: Cryo-EM structure of VGLUT3 in apo state
Authors: Qu, Q.H. / Chao, Y.L. / Yang, C.H. / Wang, X. / Zhou, Z.X.
History
DepositionAug 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vesicular glutamate transporter 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7725
Polymers60,0911
Non-polymers1,6814
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 Vesicular glutamate transporter 3 / VGluT3 / Solute carrier family 17 member 8


Mass: 60090.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc17a8, Vglut3 / Production host: Homo sapiens (human) / References: UniProt: Q8BFU8
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H50O4
Has ligand of interestN
Has protein modificationY

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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: Cryo-EM structure of VGLUT3 in apo state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
9PHENIX1.19.2_4158:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136730 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034374
ELECTRON MICROSCOPYf_angle_d0.5265964
ELECTRON MICROSCOPYf_dihedral_angle_d4.093630
ELECTRON MICROSCOPYf_chiral_restr0.041675
ELECTRON MICROSCOPYf_plane_restr0.004757

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