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Yorodumi- PDB-8wll: Cryo-EM structure of human VMAT2 Y422C, in the presence of reserp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wll | ||||||
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Title | Cryo-EM structure of human VMAT2 Y422C, in the presence of reserpine, determined in an inward-facing conformation | ||||||
Components | Synaptic vesicular amine transporter | ||||||
Keywords | TRANSPORT PROTEIN / Human VMAT2 Y422C / reserpine / Inward-facing conformation | ||||||
Function / homology | Function and homology information serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity ...serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / serotonin uptake / dopaminergic synapse / dopamine transport / monoamine transmembrane transporter activity / histamine secretion by mast cell / monoamine transport / Na+/Cl- dependent neurotransmitter transporters / neurotransmitter transport / negative regulation of reactive oxygen species biosynthetic process / response to amphetamine / post-embryonic development / secretory granule membrane / locomotory behavior / terminal bouton / response to toxic substance / synaptic vesicle membrane / synaptic vesicle / chemical synaptic transmission / axon / intracellular membrane-bounded organelle / centrosome / dendrite / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å | ||||||
Authors | Qu, Q. / Wang, Y. / Zhou, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human VMAT2 Y422C, in the presence of reserpine, determined in an inward-facing conformation Authors: Qu, Q. / Wang, Y. / Zhou, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wll.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wll.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 8wll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wll_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8wll_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8wll_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 8wll_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/8wll ftp://data.pdbj.org/pub/pdb/validation_reports/wl/8wll | HTTPS FTP |
-Related structure data
Related structure data | 37623MC 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: 53763.152 Da / Num. of mol.: 1 / Mutation: Y422C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC18A2, SVMT, VMAT2 / Cell (production host): HEK293F / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q05940 |
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#2: Chemical | ChemComp-YHR / |
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: Complex of vesicular Monoamine Transporter 2 and Reserpine Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132817 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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