+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60254 | |||||||||
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Title | Vesamicol-bound VAChT | |||||||||
Map data | ||||||||||
Sample |
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Keywords | VAChT / SLC18A3 / Vesamicol / Acetylcholine / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information acetylcholine:proton antiporter activity / acetylcholine uptake / positive regulation of neuromuscular junction development / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / 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 / positive regulation of neuromuscular junction development / clathrin-sculpted acetylcholine transport vesicle membrane / acetylcholine transmembrane transporter activity / 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 / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of long-term synaptic potentiation / 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 | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zhang Z / Zhang Y / Dai F / Zhang YX / Lee C-H | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2024 Title: Structural insights into VAChT neurotransmitter recognition and inhibition. Authors: Yang Zhang / Fei Dai / Nanhao Chen / Dong Zhou / Chia-Hsueh Lee / Chen Song / Yixiao Zhang / Zhe Zhang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60254.map.gz | 117.8 MB | EMDB map data format | |
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Header (meta data) | emd-60254-v30.xml emd-60254.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_60254.png | 160.6 KB | ||
Filedesc metadata | emd-60254.cif.gz | 6 KB | ||
Others | emd_60254_half_map_1.map.gz emd_60254_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60254 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60254 | HTTPS FTP |
-Validation report
Summary document | emd_60254_validation.pdf.gz | 943.3 KB | Display | EMDB validaton report |
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Full document | emd_60254_full_validation.pdf.gz | 942.9 KB | Display | |
Data in XML | emd_60254_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_60254_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60254 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60254 | HTTPS FTP |
-Related structure data
Related structure data | 8zmrMC 8zmsC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_60254.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_60254_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60254_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : VAChT
Entire | Name: VAChT |
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Components |
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-Supramolecule #1: VAChT
Supramolecule | Name: VAChT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Molecular weight | Theoretical: 60 KDa |
-Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetyl...
Macromolecule | Name: Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 112.70518 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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: vesamicol
Macromolecule | Name: vesamicol / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1LWL |
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Molecular weight | Theoretical: 259.386 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.25 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 184473 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |