+Open data
-Basic information
Entry | Database: PDB / ID: 8zmr | ||||||
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Title | Vesamicol-bound VAChT | ||||||
Components | Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPinoff7 | ||||||
Keywords | TRANSPORT PROTEIN / VAChT / SLC18A3 / Vesamicol / Acetylcholine | ||||||
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 (E. coli) Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Zhang, Z. / Zhang, Y. / Dai, F. / Zhang, Y.X. / Lee, C.-H. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zmr.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zmr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8zmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zmr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8zmr_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8zmr_validation.xml.gz | 26 KB | Display | |
Data in CIF | 8zmr_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/8zmr ftp://data.pdbj.org/pub/pdb/validation_reports/zm/8zmr | HTTPS FTP |
-Related structure data
Related structure data | 60254MC 8zmsC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 112705.180 Da / Num. of mol.: 1 / Mutation: A520E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others) Gene: malE, b4034, JW3994, SLC18A3, VACHT / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: Q16572 |
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#2: Chemical | ChemComp-A1LWL / Mass: 259.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25NO |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: VAChT / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Value: 0.06 MDa / Experimental value: NO | ||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||
Buffer solution | pH: 7.25 | ||||||||||||||||
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184473 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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