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- EMDB-66010: Cryo-EM structure of VGLUT3 in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-66010
TitleCryo-EM structure of VGLUT3 in apo state
Map data
Sample
  • Complex: Cryo-EM structure of VGLUT3 in apo state
    • Protein or peptide: Vesicular glutamate transporter 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordsvesicle / glutamate transporter / apo state / TRANSPORT PROTEIN
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
Vesicular glutamate transporter 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsQu QH / Chao YL / Yang CH / Wang X / Zhou ZX
Funding support China, 1 items
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 QH / Chao YL / Yang CH / Wang X / Zhou ZX
History
DepositionAug 29, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66010.png

Downloads & links

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Map

FileDownload / File: emd_66010.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 260 pix.
= 213.72 Å		0.82 Å/pix.
x 260 pix.
= 213.72 Å		0.82 Å/pix.
x 260 pix.
= 213.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.462976 - 3.8886077
Average (Standard dev.)-0.0006168532 (±0.0778895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 213.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66010_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_66010_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 : Cryo-EM structure of VGLUT3 in apo state

EntireName: Cryo-EM structure of VGLUT3 in apo state
Components
  • Complex: Cryo-EM structure of VGLUT3 in apo state
    • Protein or peptide: Vesicular glutamate transporter 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Cryo-EM structure of VGLUT3 in apo state

SupramoleculeName: Cryo-EM structure of VGLUT3 in apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Vesicular glutamate transporter 3

MacromoleculeName: Vesicular glutamate transporter 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 60.090598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPFKAFDTFK EKILKPGKEG VKNAVGDSLG ILQRKIDGTN EEEDAIELNE EGRPVQTSRA HRPVCDCSCC GIPKRYICDC SCCGIPKRY IIAVMSGLGF CISFGIRCNL GVAIVEMVNN STVYVDGKPE IQTAQFNWDP ETVGLIHGSF FWGYIVTQIP G GFISNKFA ...String:
MPFKAFDTFK EKILKPGKEG VKNAVGDSLG ILQRKIDGTN EEEDAIELNE EGRPVQTSRA HRPVCDCSCC GIPKRYICDC SCCGIPKRY IIAVMSGLGF CISFGIRCNL GVAIVEMVNN STVYVDGKPE IQTAQFNWDP ETVGLIHGSF FWGYIVTQIP G GFISNKFA ASRVFGAAIF LTSTLNMFIP SAARVHYGCV MGVRILQGLV EGVTYPACHG MWSKWAPPLE RSRLATTSFC GS YAGAVVA MPLAGVLVQY IGWASVFYIY GMFGIIWYMF WLLQAYECPA AHPTISNAER TYIETSIGEG ANLASLSKFN TPW RRFFTS LPVYAIIVAN FCRSWTFYLL LISQPAYFEE VFGFAISKVG LLSAVPHMVM TIVVPIGGQL ADYLRSRKIL TTTA VRKIM NCGGFGMEAT LLLVVGFSHT KGVAISFLVL AVGFSGFAIS GFNVNHLDIA PRYASILMGI SNGVGTLSGM VCPLI VGAM TKHKTREEWQ NVFLIAALVH YSGVIFYGVF ASGEKQDWAD PSRLEEELRR RTEPGSENLY FQ

UniProtKB: Vesicular glutamate transporter 3

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 136730
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

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

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