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- EMDB-62394: Cryo-EM structure of human VAChT in apo state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62394
TitleCryo-EM structure of human VAChT in apo state
Map data
Sample
  • Complex: VAChT
    • Protein or peptide: Soluble cytochrome b562,Vesicular acetylcholine transporter
Keywordstransporter / VAChT / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZhang W / Wei F / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human VAChT in apo state
Authors: Zhang W / Wei F / Zhang Y
History
DepositionNov 14, 2024-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62394.png

Downloads & links

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Map

FileDownload / File: emd_62394.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.844101 - 2.9340532
Average (Standard dev.)-0.0010028926 (±0.066561386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62394_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62394_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 : VAChT

EntireName: VAChT
Components
  • Complex: VAChT
    • Protein or peptide: Soluble cytochrome b562,Vesicular acetylcholine transporter

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Supramolecule #1: VAChT

SupramoleculeName: VAChT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Soluble cytochrome b562,Vesicular acetylcholine transporter

MacromoleculeName: Soluble cytochrome b562,Vesicular acetylcholine transporter
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.325781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADLEDNWET LNDNLKVIEK ADNAAQVKDA LTKMRAAALD AQKATPPKLE DKSPDSPEMK DFRHGFDILV GQIDDALKLA NEGKVKEAQ AAAEQLKTTR NAYIQKYLLQ EPRRQRRLVL VIVCVALLLD NMLYMVIVPI VPDYIAHMRG GGEGPTRTPE V WEPTLPLP ...String:
MADLEDNWET LNDNLKVIEK ADNAAQVKDA LTKMRAAALD AQKATPPKLE DKSPDSPEMK DFRHGFDILV GQIDDALKLA NEGKVKEAQ AAAEQLKTTR NAYIQKYLLQ EPRRQRRLVL VIVCVALLLD NMLYMVIVPI VPDYIAHMRG GGEGPTRTPE V WEPTLPLP TPANASAYTA NTSASPTAAW PAGSALRPRY PTESEDVKIG VLFASKAILQ LLVNPLSGPF IDRMSYDVPL LI GLGVMFA STVLFAFAED YATLFAARSL QGLGSAFADT SGIAMIADKY PEEPERSRAL GVALAFISFG SLVAPPFGGI LYE FAGKRV PFLVLAAVSL FDALLLLAVA KPFSAAARAR ANLPVGTPIH RLMLDPYIAV VAGALTTCNI PLAFLEPTIA TWMK HTMAA SEWEMGMAWL PAFVPHVLGV YLTVRLAARY PHLQWLYGAL GLAVIGASSC IVPACRSFAP LVVSLCGLCF GIALV DTAL LPTLAFLVDV RHVSVYGSVY AIADISYSVA YALGPIVAGH IVHSLGFEQL SLGMGLANLL YAPVLLLLRN VGLLTR SRS ERDVLLDEPP QGLYDAVRLR ERPVSGQDGE PRSPPGPFDA CEDDYNYYYT RSHHHHHHHH HHGSVEDYKD DDDK

UniProtKB: Soluble cytochrome b562, Vesicular acetylcholine transporter

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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

Concentration10 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 113960
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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