[English] 日本語
Yorodumi
- EMDB-66019: Alkylsulfone-bound human VAChT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66019
TitleAlkylsulfone-bound human VAChT
Map data
Sample
  • Complex: human VAChT in complex with alkylsulfone
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPins
  • Ligand: 2-(3-ethylsulfonylpyridin-2-yl)-3-methyl-6-(trifluoromethyl)imidazo[4,5-b]pyridine
KeywordsVAChT / SLC18A3 / Acetylcholine / Alkylsulfone / TRANSPORT PROTEIN
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 speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang Z / Zhang Y
Funding support China, 1 items
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, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66019.png

Downloads & links

-
Map

FileDownload / File: emd_66019.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-3.2390983 - 4.1193056
Average (Standard dev.)0.00042033664 (±0.03683148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_66019_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66019_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human VAChT in complex with alkylsulfone

EntireName: human VAChT in complex with alkylsulfone
Components
  • Complex: human VAChT in complex with alkylsulfone
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPins
  • Ligand: 2-(3-ethylsulfonylpyridin-2-yl)-3-methyl-6-(trifluoromethyl)imidazo[4,5-b]pyridine

-
Supramolecule #1: human VAChT in complex with alkylsulfone

SupramoleculeName: human VAChT in complex with alkylsulfone / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

-
Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetyl...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPins
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 112.70518 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEITP DKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN LQEPYFTWPL I AADGGYAF ...String:
MEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEITP DKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN LQEPYFTWPL I AADGGYAF KYENGKYDIK DVGVDNAGAK AGLTFLIDLI KNKHMNADTD YSIAEAAFNK GETAMTINGP WAWSNIDTSK VN YGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EELVKDPRVA ATM ENAQKG EIMPNIPQMS AFWYAVRTAV INAASGRQTV DAALAAAQAE EEKRKAEEEK RKLVLVIVCV ALLLDNMLYM VIVP IVPDY IAHMRGGGEG PTRTPEVWEP TLPLPTPANA SAYTANTSAS PTAAWPAGSA LRPRYPTESE DVKIGVLFAS KAILQ LLVN PLSGPFIDRM SYDVPLLIGL GVMFASTVLF AFAEDYATLF AARSLQGLGS AFADTSGIAM IADKYPEEPE RSRALG VAL AFISFGSLVA PPFGGILYEF AGKRVPFLVL AAVSLFDALL LLAVAKPFSA AARARANLPV GTPIHRLMLD PYIAVVA GA LTTCNIPLAF LEPTIATWMK HTMAASEWEM GMAWLPAFVP HVLGVYLTVR LAARYPHLQW LYGALGLAVI GASSCIVP A CRSFAPLVVS LCGLCFGIAL VDTALLPTLA FLVDVRHVSV YGSVYAIADI SYSVAYALGP IVAGHIVHSL GFEQLSLGM GLANLLYAPV LLLLRNVGLL TRSRSERDVL LDEPPQGLYD AVRLRERPVS GQDGEPRSPP GPFDECEDDG GGGSGGGGSD LGRKLLEAA RAGQLDEVRI LLANGADVNA ADNTGTTPLH LAAYSGHLEI VEVLLKHGAD VDASDVFGYT PLHLAAYWGH L EIVEVLLK NGADVNAMDS DGMTPLHLAA KWGYLEIVEV LLKHGADVNA QDKFGKTAFD ISIDNGNEDL AEILQKLNLE GG SLEVLFQ

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Vesicular acetylcholine transporter

-
Macromolecule #2: 2-(3-ethylsulfonylpyridin-2-yl)-3-methyl-6-(trifluoromethyl)imida...

MacromoleculeName: 2-(3-ethylsulfonylpyridin-2-yl)-3-methyl-6-(trifluoromethyl)imidazo[4,5-b]pyridine
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EWW
Molecular weightTheoretical: 370.35 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 7.25
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 210095
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more